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A Critical Conversion Divergence

Chapter Text

Rodney’s head jerked up from the console he was working on as he heard Elizabeth’s announcement of a security breach at Colonel Sheppard’s quarters. Abandoning his current work, he moved to another console, his fingers flying as he worked to track down his team leader. With the majority of his attention focused on his work he was still vaguely aware of the personnel gathering in the control room. He rolled his eyes as Caldwell stormed into the room, shouting demands.

Find Sheppard. Immediately!”

Yes, yes, what do you think I’m doing here, playing Free-cell?” Rodney muttered as he continued to work. His attention still mainly on his task, Rodney was nevertheless aware of and slightly relieved by the arrival of his other two teammates. “And there,” he announced as he stood and moved to a large display showing a moving dot. “We’ve got a lock on him.”

That can’t be him. It’s moving too fast,” Caldwell stated in disbelief.

It’s him,” Ronon replied.

Caldwell turned and addressed the Marines. “All right. Four teams. Surround him and close in. I want him stopped, and gentlemen use whatever level of force you deem necessary. Move out.”

You will only use such force as a last resort,” Elizabeth said firmly.

The Marines had paused, and were now looking back and forth between the two. “That is not your call, Dr. Weir,” Caldwell told her.

Excuse me?” Elizabeth said, whirling to fix him with a cold glare.

Rodney felt his blood run cold as he observed the stare-down between the two of them. Glancing back at the Marines who still stood there waiting, he noted with a sinking feeling that they were all newcomers. None of them were from the original expedition. Would they follow Elizabeth, their boss, or would they defer to Caldwell as their superior officer. He glanced at them again and realized that a few of them were actually personnel from the Daedalus. He had a really bad feeling about this.

This is a military situation now,” Caldwell continued. “And as the ranking military officer it is my orders that will be obeyed.”

I am the leader of this expedition, I determine what is a military situation.” She turned to the Marines. “You have your orders. Use of force as a last resort only.”

Rodney watched, silently panicking as the Marines glanced at Weir before turning their attention back to Caldwell. This was so not good. Rodney grabbed his tablet and began to edge toward the back of the room and the transporter located there.

I think that you are too close to the situation and are letting your emotions cloud your judgment. That thing is no longer Colonel Sheppard and has to be stopped. Those bruises on your neck are evidence of that.” Caldwell turned back to the Marines. “You have your orders.”

Yes sir,” they said, saluting him quickly before turning and heading for the stairs, ignoring Elizabeth’s protests.

Screw this,” Ronon growled as he started to follow them, Teyla on his heels. They were stopped by the remaining soldiers at a signal from Caldwell. “Move,” Ronon demanded, a dangerous air about him.

I can’t allow you two to participate in the search. Like Dr. Weir you are too close to Sheppard and thus emotionally compromised.”

I’ll show you compromised,” Ronon growled, his hand moving to his gun before he collapsed, felled from behind by a shot from a Wraith stunner.

Elizabeth and Teyla both began protesting this action loudly, as the soldier turned the stunner in their direction but didn’t fire. Yet . Rodney found himself frozen, just a short distance from the transporter, speechless for once in his life.

The radio in the control room activated with a report that the first team had encountered Sheppard but had been unable to stop him. The news that the Wraith stunners had no effect chilled Rodney to the bone while at the same time it broke through his paralysis and he continued backing up to the transporter. He glanced at the display of his tablet, noting as Sheppard’s dot shifted locations. He quickly used his tablet to disable most of the transporters in Sheppard’s new location.

Caldwell glanced briefly at Elizabeth as if to say I told you so, then activated his headset. “All search teams, stunners do not work. Don’t waste your time trying to use them. Remember, the use of lethal force is authorized.”

Oh shit’, Rodney thought as he reached the transporter and input his command code. Thankfully the noise in the control room covered the sound of the doors sliding open. His eyes met Teyla’s and she gave him a slight nod as he reached for the transporter’s map. As the doors closed, he heard Caldwell issuing orders for Elizabeth, Teyla and Ronon to be locked up inside the conference room under guard.

Sometimes I really hate being right,” he muttered as he exited the last working transporter near Sheppard’s current location. He quickly disabled it as well, then reached for his radio. “Carson.”

Rodney! What’s going on?” Came the accented reply.

There’s no time. Caldwell’s gone power hungry. He locked Elizabeth, Ronon and Teyla up and ordered the military to use lethal force to stop Sheppard. They’re going to kill him,” Rodney stated with certainty.

What?! That cannae be right.”

I don’t have time to argue. I need you and a medical team to get to the corridor outside sector 5 in Tower 3. You’ll have to take the long way as the transporters are disabled. And be prepared for anything.”

Rodney, where are ye?”

Where do you think? Someone’s got to get to Sheppard before they kill him.”


Just get to that corridor, McKay out!” He turned off his radio, cutting off Beckett’s protest, and swallowed hard. “Okay McKay, you can do this. It’s your turn to save Sheppard.” He glanced at his tablet to confirm Sheppard’s location, then closed his eyes and lightly banged his head against the wall. “I have lost my mind.” He must have, to be considering this insane action. It wasn’t too late, he could still change his mind. Then he thought about Sheppard and what would likely happen if he didn’t do this. No, he couldn’t leave Sheppard to the fate that awaited him. He knew the other man wouldn’t do that if their positions were reversed. “Okay, time to go.” He quickly made his way to the room Sheppard was currently in.

Upon reaching the room he noted that his and Sheppard’s life signs were the only ones nearby at the moment. He quickly gathered his courage and stepped into the room. “Colonel? Colonel Sheppard?” Of course there was no response.

Sheppard! It’s me, Rodney. Rodney McKay. Dr. Rodney McKay.” Still no response. Not that he was really expecting one. Okay, he hoped for one but- he forced those thoughts away and glanced at his tablet and frowned. He should be right on top of the man.

Look, Caldwell’s gone nuts and we have to get you to safety before his men find you. Would you just- GAH!” His words cut off with a shriek as there was a thump behind him and suddenly he found himself grabbed and shoved against a wall, his tablet slipping from his fingers with a clatter. Realizing he had closed his eyes, he opened them and for the first time laid eyes on the changed man.

Blue scales crept up his neck and spread over his lower face. Clawed, scaly hands were clenching Rodney’s jacket, holding him against the wall. His hazel eyes were now slitted like a cat’s as they gazed back into Rodney’s blue ones. But he thought he could still see some intelligence there, some glimmer of the John Sheppard he knew.

Sheppard, it’s me, Rodney.” He swallowed thickly as Sheppard made a chittering noise and pressed him harder into the wall. “Oh please, we both know you’re not going to hurt me. You haven’t once in the time we’ve known each other despite the urge I know you get periodically. You won’t now,” Rodney stated with bravado, hoping it was the truth.

Sheppard cocked his head to one side, one eyebrow lifting as he studied Rodney.

It was such a Sheppard expression that it, combined with their position (a position that featured in many of Rodney’s secret fantasies), and despite the situation and Sheppard’s alien features, caused Rodney’s body to react. He swallowed thickly as he tried to will his body’s response away. ‘Crap,’ he thought as Sheppard pressed even closer. “Sheppard. John.” He tried again to reach the man before him, reminding him of how they knew each other, their missions, hanging out together, playing the Game, hoping he got through.


John cocked his head and lifted an eyebrow as the man he had pinned to the wall continued to babble at him. He ignored the words, finding it too hard to concentrate on their meaning. Instead he focused on the man himself. The man was familiar to him, extremely familiar. But his head was so clouded and it was hard to concentrate on how he knew him. However, unlike the other men he had encountered recently it was obvious that this man was no threat.

He sniffed carefully but there was only a slight hint of that wrong scent he had been picking up from the others he encountered. Beneath that trace of wrong was a not unpleasant scent, one that seemed familiar, just like this man was familiar.

John leaned forward suddenly, pressing the other man further into the wall as a new scent reached his nose. He couldn’t get enough of that scent and he leaned forward more, shoving his face into the man’s neck, breathing that intoxicating scent in. He felt the man’s hardness against his thigh and realization filtered slowly through his clouded mind as the babble of words increased in pace and pitch. This man belonged to him. That was why he was so familiar. This man was his.

But before John could act on his realization his senses told him of others approaching. He spun around, placing himself protectively in front of the other man. Rodney , his mind whispered to him. He glared at the two men who stood in the doorway pointing what his mind told him were weapons at him and Rodney.

No, no, no! Don’t shoot! Look you idiots, he’s not attacking, not hurting anyone. Give me a little longer and I’m sure I can get him to surrender. Don’t shoot!”

John heard Rodney’s words but ignored them, his focus on the danger in front of him. How could he reach them before they were able to use their weapons against him and Rodney? He felt Rodney try to push past him, and shoved him back behind him, chittering angrily at him. Didn’t the fool know not to make himself a target? He kept one hand on him, pulling him along as he tried to move them to some type of cover.

No! Can’t you see he’s trying to protect me?! For god's sake don’t shoot!”

One of the newcomers said something and John hissed at him. There was a sudden loud, echoing noise (gunshots, his mind supplied) just as John felt himself shoved to the ground. Pain burned through his arm, angering him and he quickly threw himself at his attackers before they could fire again, his speed too fast for them to compete with as he threw them roughly against the wall, knocking them unconscious. He glanced at his right arm and hissed at the damage, blood dripping down to the ground.

He became aware of the silence in the room and that was wrong. Why wasn’t Rodney babbling anymore? His mind told him that a silent Rodney was a bad thing. He quickly turned to where he had left Rodney and froze for a moment as a keening wail burst harshly from his throat.

Rodney lay on the ground where he had fallen after shoving John out of the line of fire. He lay unmoving, a puddle of blood spreading out beneath him from a wound high in his chest. Weak, pain-filled gasps filled the air as he struggled to get oxygen into his damaged body. Each hard-won breath obviously caused him more pain. His head tilted in John’s direction. “Sheppard, John,” he called out weakly before his eyes rolled up in to the back of his head.

Just like that John’s paralysis was broken and he was instantly kneeling at Rodney’s side. Another broken sound escaped him as he took in the damage up close. Too much damage. No, he couldn’t let it end like this. ‘Stop the bleeding,’ his mind whispered to him and he reached out, pressing down on the wound on Rodney’s chest, noticing but not caring as their blood mixed together as he tried to keep the much needed liquid inside the other man’s body. “Rodney,” he rasped out, over and over again.



Carson paced in the corridor Rodney had directed him to. The bloody fool wasn’t answering any radio calls. What happened to the man who was a coward, valuing his own safety and well-being over others? Carson sighed. That man had never really existed, had only existed as a front to protect others from seeing just how much he cared. But to put himself in such a dangerous situation; the man really had changed.

Carson froze as gunshots echoed from the section beyond the corridor he and his medical team waited in. “Wait here, I’ll go check it out,” he told the rest of his team.

But Dr. Beckett-” one of the nurses began to protest.

No, no sense in risking all of our lives. I’ll radio if the situation is safe and further assistance is necessary, so please wait here.” He waited for their reluctant nods, then grabbed one of the emergency medical kits, girded his loins (figuratively) and entered the section of the city where he would, hopefully, find his friends alive and well.

As he proceeded further into this unoccupied section of the city, he thought ruefully to himself that Rodney wasn’t the only bloody fool around.

An inhuman wail suddenly filled the air, startling him into nearly dropping the medical kit. It cut off quickly. “Yer a bloody fool Carson,” he muttered to himself even as he hurried further in the direction the sound had come from.

Slipping into the wide room he noticed two Marines from the Daedalus lying near the doorway and was about to check on them when movement further in the room caught his eye. His breath caught in his throat as he took in the figures huddled on the floor and the massive puddle of blood surrounding them.

No,” he gasped out, even as he began to move toward them, the unconscious Marines forgotten in the face of a more serious medical emergency.

One of the figures lifted his head at his approach and a snarl escaped him. Carson froze at the sound and the sight of those slitted eyes glaring at him. Then the figure tilted his head, studying him. “Doc,” he rasped out.

Aye Colonel, it’s me. Carson.”

The Colonel lifted one of his blood stained hands from the too still figure and gestured Carson closer. “Help. Rodney. Help,” Sheppard rasped out, as if it was taking all of his concentration just to get those words out.

Carson was amazed that Sheppard was even this lucid at this point but quickly shook the thought away as unimportant at the moment. He hurried the rest of the way to the two men and knelt beside Sheppard as he pulled on a pair of gloves. Dismay filled him as he gestured for Sheppard to move his hands and he was able to see just where the wound was. It was too close to Rodney’s heart, and even if he was able to get him to the infirmary quickly enough, judging by the amount of blood surrounding them it did not seem possible that Rodney would survive the necessary surgery.

Carson lifted his head and met those alien eyes. “I’m sorry, I dinnae think there is anything I can do.” Tears stung his eyes at the admission.

No! Help! Rodney!” Desperation and despair filled the Colonel’s voice and face.

Unable to keep meeting Sheppard’s gaze in such an emotional moment, Carson instead lowered his eyes to Rodney. And frowned as his mind registered something strange. Was it his imagination or was Rodney’s breathing becoming easier? The breaths should be raspier and harsher as the end approached and yet they seemed to be getting smoother instead.

He glanced at the wound on Rodney’s chest and did a double take. Was that? It was!

The wound was getting smaller.

But how? How was this possible?

Carson lifted his head to ask the only other conscious person present if he was imagining things when his eyes landed on Sheppard’s arm and a detail he hadn’t noticed before made itself known. Specifically, the wound on the Colonel’s arm and the blood that was dripping down that arm, though obviously at a much slower rate then it must have been earlier. The arm that had not too long ago been applying pressure to Rodney’s more serious wound.

Oh bloody hell.” Just as Elia had infected the Colonel through an open wound and it had healed, now the Colonel’s changed blood had infected and was now healing Rodney.

Sheppard stared at him hopefully. “Help?”


Aye, I’ll help. Here, let’s shift him on his side. I need to make sure there’s an exit wound or we’ll have to remove the bullet.” With the Colonel’s help he was able to quickly determine that yes, there was an exit wound which was also rapidly healing.


Okay, I’m going to radio the rest of my team. We need to get you lads to the infirmary right away.” Carson swallowed as he wondered if the retrovirus had saved his friend’s life only to take him away anyway. After all, he hasn’t been able to cure the Colonel and now Rodney was facing the same fate. And yet, he thought glancing at the obviously worried man beside him, some part of the Colonel was still present. Perhaps not all was lost yet after all. He reached for his headset to suit actions to words only to freeze at the sound of a cocked.


I wouldn’t do that if I were you Doctor.”

Chapter Text

Major Evan Lorne strode into the control room, his face carefully blank to mask his concern over the reports he had received. His main concern should have been for his missing Commanding Officer, the one he should have been out looking for. And yet, the reports he had received had filled him with the belief that there was something else just as wrong in the city. “Sir,” he said with a quick salute to Colonel Caldwell.

The Colonel frowned at him. “Shouldn’t you be out on a search team Major?”

I was on my way to join Bravo team, sir, when I heard something worrying. Is it true that you ordered Dr. Weir, as well as Teyla and Ronon, locked up?”

The Colonel’s frown deepened. “I had them detained as they are too emotionally compromised by this situation. The last thing we need is someone getting hurt because of sentiment. I wonder if perhaps you yourself might need to step back from this situation.”

Evan forced himself to stay relaxed and keep his face free from emotion. “No, sir! I just wanted to make sure of the situation. I know how to follow orders. And what about Dr. McKay?”

What about him?”

Is he also detained?”

The Colonel snorted derisively. “That coward? Please, do you really think he’s going to risk his own neck by getting involved in this situation? No, he did what needed to be done in helping to locate Sheppard and prevent him from escaping, then crawled away to hide, unable to face the situation.”

Evan carefully kept the frown off his face. Once, when he first arrived he might have agreed with the Colonel about the loud-mouthed Doctor but he had seen how, despite his complaining, the man continued to put himself in life-threatening situations for the good of others. Hell, just earlier today he had entered an Iratus nest in search of a cure for Sheppard, granted not without complaining but he had still done it. “Yes, sir. Would you like me to arrange for a guard for Dr. Weir and the others?”

Already taken care of.” The Colonel waved him off. “Finally,” he said as a tech came over and handed him a tablet. “Here, we’ve finally managed to tap into the security footage for the area Sheppard’s in and it appears that Woods and Michaelson are nearly there.”

Evan stepped closer in order to also view the footage but he frowned at the names mentioned. Those were not Atlantis personnel. They were from the Daedalus. Why had the Colonel sent men from the Daedalus instead of Atlantis?

There’s Sheppard. What the hell?!”

I guess Dr. McKay decided to risk his own neck after all,” Evan said blandly as he studied the footage. Sheppard had McKay pinned to the wall but from what he could see he hadn’t hurt him. McKay was obviously talking, big surprise there, though there was no audio to go with the footage. Perhaps the scientist would be able to talk Colonel Sheppard into surrendering.

God damn it! This is exactly why I didn’t want anyone who was emotionally compromised involved. Now we’re going to have additional casualties.”

Evan stiffened slightly at the Colonel’s implication that Colonel Sheppard’s death was a certainty. “He doesn’t appear to be harming Dr. McKay,” he pointed out instead. “Perhaps Woods and Michaelson should wait, see if this can be resolved without anyone getting hurt.”

But the Colonel ignored him, tapping his radio. “Woods, Michaelson, you’re nearly there. Hurry it up, Sheppard’s got McKay hostage.”


The Colonel shot him a look. “Did I ask your opinion Major?”

No sir.” Evan stood there stiffly, watching the display as the two Marines entered the room, weapons drawn. His eyebrows rose as Sheppard clearly placed himself protectively in front of McKay. “I really think they should back off sir.”

Caldwell ignored him as he keyed his radio. “Take him down,” he ordered.

One of the men, Michaelson, replied. “What about McKay?”

It’s his own fault for putting himself in this situation. We have to stop that thing. You have your orders.”

Evan knew that at this point it was futile to continue to protest and could only watch with growing horror as the two men opened fire on his CO and the scientist. He watched as McKay shoved Colonel Sheppard out of the line of fire only to be hit himself. Sheppard’s mutated form was clearly stronger and faster as he was able to take out the two men before they could fire again.

God damn it!” Caldwell swore and punched a wall, denting it to Evan’s surprise. He ordered more men to that section only to be told that it would take a while without the transporters. “Someone get a transporter up and running, fast. We need to secure that area before Sheppard escapes again!” he ordered the wide-eyed techs in the control room.

What about getting a medical team there?” Evan questioned. “Dr. McKay looks to be badly wounded, not to mention Woods and Michaelson could probably use help as well.”

Caldwell shot him a look. “What the hell are you still doing here Major?! Why aren’t you getting a team together to go secure that area?”

Evan stiffened. “Yes sir, I’ll go do that right away.” He saluted, turned and walked away. The Colonel wanted him to put together a team and he knew just who to ask.

Once out of sight and earshot of the control room he keyed his headset to one of the science channels, hoping Colonel Caldwell was too busy monitoring the military channels to pay attention to this one. “Lorne to Zelenka.”


Switch to channel 5,” he told him, referring to one of the private channels set up for command staff. Even if Caldwell wasn’t monitoring the science channels someone else could overhear and report it to him. This would hopefully be safe enough.

Yes, Major?” Zelenka asked once he had switched over.

Hey Dr. Z. I need a favor. I need you to stall on reactivating the transporters. Delay the teams from reaching the section where Colonel Sheppard is. But I also need to be able to get there quickly myself.”

What is going on Major?”

Dr. McKay is badly injured and Colonel Caldwell doesn’t seem concerned about that or any other injuries that may occur.” Evan had to pause as Czech curses filled the transmission. “I’m trying to prevent that from happening but I need your help.”

Done. I will delay them. I have one transporter operating in that section though computers think it is not. Good luck Major and hurry.”

I am, just need to get some people and we’ll be on our way. Lorne out.” He ended the transmission and quickly headed toward the conference room, stopping only to retrieve Ronon’s energy weapon.

Sergeant,” he greeted the man guarding the door, who stiffened at his approach.


I’ll take it from here. Why don’t you take a break?”

The Sergeant, Rollins, Evan recalled, hesitated. “I have orders from Colonel Caldwell not to leave this post. Sir,” he said in an apologetic tone.

Evan nodded. “And I have orders of my own from the Colonel.” Not technically a lie. After all, he had never said who to gather for his team. The Sergeant stared at him for a long moment, considering Evan’s words and Evan held his breath, waiting. As the man finally relaxed, Evan suppressed a sigh of relief, silently thanking his reputation as a by the book officer who always followed orders.

Yes sir,” Rollins said as he walked away with a nod of acknowledgment.

Evan knew he had lucked out, Rollins really should have contacted Colonel Caldwell to confirm Evan’s orders. He assumed that the other man felt as conflicted by recent events as he did. Still, he spared a brief moment to pray that he wasn’t screwing up both of their careers with this course of action then triggered the door release.

And immediately had to jump back as Ronon threw himself at him. “Whoa! Easy big guy, I’m on your side!” He held up his hands to show he meant them no harm.

Ronon glared but stopped trying to attack. For the moment anyway. His body was tense, obviously ready to act at a second’s notice.

Major, what is going on?” Dr. Weir asked as she and Teyla joined them in the doorway.

There’s not a lot of time to explain. Short version is that I can’t agree with Colonel Caldwell’s actions. I saw some of the security footage and it is obvious that some part of Colonel Sheppard is still present and could be reasoned with but Colonel Caldwell isn’t listening to reason. Dr. McKay has already been badly injured, we need to hurry before it’s too late.” Evan specifically looked toward Teyla and Ronon. “I’ll need your help, you’re probably the ones with the best chance of reaching Sheppard and keeping him from reacting badly.” He handed Ronon his weapon and gestured for them to come with him.

I’m coming too,” Dr. Weir stated as she moved to follow them.

Ma’am I really don’t believe that is a good idea. It won’t be safe for you there.” Evan really did not need the complication her presence would cause.

She fixed him with a look. “We don’t have time to argue about this, I’m going and that’s final.”

Ma’am,” he started to say only to be interrupted by his radio.

Zelenka to Lorne.”

Lorne here,” he replied after tapping his headset.

Major, there is a problem. Colonel Caldwell must have tapped into our conversation. He has accessed the transporter I left operable for you. None of the other search teams have used it yet but you must hurry.”

Shit,” Evan swore. “Thanks for the heads up Doc.” He ended the transmission and turned back to Weir. “Alright, I don’t have time to argue, Colonel Caldwell’s on his way to Sheppard. But stay out of the line of fire,” he told her. “Let’s go.” Colonel Sheppard would have his head when he learned about this but there really was no time to argue.

They quickly headed to the nearest transporter, praying they would make it in time.



Let’s not be hasty Colonel,” Carson said soothingly as he held up his hands. Beside him Colonel Sheppard tensed, his nostrils flaring before he began to hiss quietly. At any other time, Carson would have been fascinated by the changes in his physiology that allowed him to produce such inhuman sounds but this was not the time for those thoughts. He kept his attention focused on the current threat in the room. “As you can see Colonel Sheppard is not currently a threat. We need to get him and Rodney to the infirmary immediately.”

What I see Doctor, is two civilians who obviously don’t know how to follow orders or keep themselves out of a dangerous situation. Sadly Dr. McKay will pay the price of his foolishness, after having been attacked by Sheppard.”

What?! Are ye blind man?! Rodney was shot! By your men!”

Yes, after they tried to save him from Sheppard’s attack and he stupidly put himself in the line of fire. Are you that stupid as well?” Caldwell asked, the gun being aimed slightly in Carson’s direction while still covering Sheppard.

Carson swallowed nervously but before he could reply Sheppard rose to his feet and slowly took a few steps away from Carson and Rodney. The gun in Caldwell’s hand followed his movement.

That’s far enough. I’d tell you to say your goodbyes but I think that’s beyond you at this point.” Smugness colored the Colonel’s voice and a look of utter arrogance covered his face.

Carson found his voice again. “Ye can’t do this, it’s murder!”

You don’t get to tell me what I can and can’t do. I am going to deal with this abomination once and for all.”

This is wrong,” Carson said, shaking his head and moving to stand up. He stopped at Colonel Sheppard’s hiss and head shake.

Listen to the freak Doctor. It would be a shame if you ended up with the same fate as Dr. McKay.”

Sheppard’s hisses increased in volume at the thinly veiled threat, his hands clenching and unclenching at his sides.

And what fate would that be Colonel?” Elizabeth stated from behind the Colonel, surrounded by Teyla, Ronon and Major Lorne.

Oh thank God,” Carson exclaimed in relief at the sight of them.

Does no one in this city know how to follow orders?!” Anger laced the Colonel’s voice as he glanced briefly back at them, moving to get them in his view without taking his eyes off of Sheppard. “I expected better of you Major.”

You told me to gather a team to go after Colonel Sheppard, you never specified who should be on it.”

Sheppard took advantage of Caldwell’s inattention to lunge at him, ignoring the shouted protests from the others. Caldwell immediately pulled the trigger but Sheppard was too fast, zigzagging out of the way until he could knock the weapon away and grab the Colonel by his throat, pushing him up against the wall in an echo of his previous actions with Elizabeth. He squeezed the Colonel’s throat while his other arm was pulled back, clawed fingers ready to strike. Major Lorne, Teyla and Ronon immediately pointed their weapons at him.

Elizabeth held up a hand, stopping them from taking any immediate action. “John,” she said, trying to project an air of calm. “You need to release him.”

John hissed, shaking his head before an angry chittering sound escaped his throat.

Again, Carson found himself vaguely contemplating the change to the Colonel’s vocal cords.

John, this isn’t solving anything.” Ever the diplomat, Elizabeth continued to try for a peaceful solution.

Wrong,” Sheppard rasped out.

Gotta say I agree with Sheppard. What?” Ronon said at the looks he received from the others. “The guy tried to kill him, I think he’s got the right idea.”

Teyla shook her head. “Colonel. Please do not make us do this.”

Sheppard glanced at her and hesitated a moment. “Smells wrong.” He tried again to explain then shook his head, his arm starting to move forward. A high pitched whine sounded and red energy surrounded him, causing him and Caldwell both to fall to the ground. Ronon fired again, leaving Sheppard lying there motionless, his eyes open.

Everyone glanced at Ronon. “What? It was set to stun.”

As everyone breathed a sigh of relief Colonel Caldwell sat up and reached for the discarded gun.

The other three with weapons immediately turned them on him.

Sir, I would suggest you rethink this course of action,” Major Lorne told him.

At this point several teams of military personnel entered the room with their weapons armed and ready, only to pause as they took in the scene. Their confusion was obvious. “Sir?” One of the team leaders asked.

Good, someone who will follow orders. Lieutenant, you are to take these people into custody to face charges of disobeying orders and interfering in a military matter.”

No,” Elizabeth interrupted. “You need to take Colonel Caldwell into custody for attempted murder.”

Having received conflicting orders the men hesitated a moment before reacting. The split was obvious once they did react, with half of them, mostly those who had been in Atlantis the longest, pointing their weapons at the Colonel while the others, mostly newcomers, pointed them at Elizabeth and the others. One even aimed at Carson where he still knelt beside Rodney. And he was getting sick of weapons being pointed at him today. “Just bloody perfect,” he muttered. A bit louder he added, “Is there any chance this could wait until after I’ve gotten my patients to the infirmary for treatment?”

The men exchanged glances, obviously considering his suggestion.

No this can’t wait!” Caldwell ground out through gritted teeth as he rose to his feet. “Lieutenant I gave you and your men an order and I expect it to be followed! That abomination,” he gave Sheppard a dirty look, “needs to be destroyed before it hurts anyone else and these people are too irrational, blinded by their emotions to see the situation clearly.”

With all due respect, Sir,” Major Lorne started, his tone clearly implying that he had little respect left for the Colonel, “the only one who is acting irrational at the moment is you. There is evidence that Colonel Sheppard was still somewhat lucid and only attacked after being threatened.”

Aye, and he was clearly trying to stop Rodney’s bleeding when I arrived,” Carson quickly added.

The Major gave him a nod of thanks before continuing. “So it makes no sense for you to keep trying to escalate the situation with violence.”

Several of the men who had been aiming at Elizabeth’s group began to lower their weapons. Colonel Caldwell lost it at this point. “I am the ranking military officer. You are supposed to listen to me and obey my orders!” He began to rant, causing several of the others who had originally obeyed him to become doubtful and start to lower their weapons as well. That was when the Colonel’s eyes glowed and his voice became deeper, echoing slightly. “I am a god! You will obey me!”

Shit, he’s a Goa’uld!” Lorne cursed as all those armed with weapons now aimed them at Caldwell.

You will bow before m-”

The words were cut off as Ronon once again decided to take matters into his own hands by shooting Caldwell. “Still set to stun,” he said, rolling his eyes at the looks directed his way. “So what’s a Goa’uld and why did his eyes and voice do that?”

A Goa’uld is a parasitical alien that takes humans as hosts,” Elizabeth answered him, slightly shaken by the knowledge that the Goa’uld had managed to reach Atlantis.

Think of it as a snake that burrows into your head and takes over your body,” Lorne added with a grimace.

That doesn’t sound pleasant,” Ronon said, eyeing Caldwell as if the Goa’uld was going to leap out of Caldwell in search of a new host.

Not a pleasant thought and yet very possible. Carson suppressed a shudder.

How the hell did this happen?” Lorne asked, shaking his head. “How was he able to get all the way out here without anyone realizing he’d been snaked?”

I don’t know but everyone on Atlantis and the Daedalus is going to have to be examined to make sure he’s the only one. No one will be exempt,” Elizabeth stated firmly.

Just wonderful, Carson thought. Couldn’t they get through one crisis at a time? At that moment Rodney began to show signs of regaining consciousness so Carson quickly checked his wound. “Bloody hell,” he muttered quietly as he took in the completely healed chest that was showing a rapidly spreading blue discoloration. The retrovirus was clearly spreading through Rodney’s body much faster than it had Colonel Sheppard’s. This was very not good.

Beckett to Biro.”

Biro here. Carson is everything alright? We were getting worried that we hadn’t heard from you.”

Aye, we had a wee bit of excitement here but everything’s under control now. I need you and the rest of the team to come in now, we’re going to need at least five gurneys.” He glanced around at the various unconscious men. “And make sure they have restraints. Lots of restraints.” About to sign off his eyes landed on Rodney’s chest. “And everyone should make sure they’re in protective gear. There’s a lot of blood, can’t risk anyone else getting contaminated by the retrovirus. Beckett out.”

Rodney regained consciousness at that moment. “Why am I on the ground?” he asked. “Carson? What’s going on?” His eyes widened as memory returned. “Sheppard!”

Easy lad, the Colonel’s okay for the moment, just stunned. Now I need you to tell me how you’re feeling.”

I was shot! How do you think I’m feeling?” Rodney snidely asked before his mouth dropped open in shock. “I was shot! Why aren’t I dead?” He started to pull at his shirt, trying to examine his chest.

Easy there Rodney, don’t do that.” Carson tried to prevent him from seeing anything to no avail.

Oh my God,” Rodney gasped out, face full of fear as he took in the lack of a wound and the presence of the blue discoloration on his chest.

Everything will be alright Rodney,” Carson tried to reassure him. ‘I hope,’ he thought as the rest of the medical team finally entered, splitting up to check each of their patients. “And this time you get a ride on a gurney,” he added weakly, recalling Rodney’s earlier complaints about having to walk. Was that really only a few days ago? It seemed so much longer.

Carson?” Elizabeth asked as she eyed the puddle of drying blood surrounding him and Rodney.

Carson sighed. “Would everyone please be careful what they touch, especially if ye have any open wounds.” He met Elizabeth’s eyes, letting her see the worry there. “It’s not only a Goa’uld that we have to check everyone for,” he told her, his eyes straying once more to Rodney’s chest.


Chapter Text

Elizabeth stood quietly in a corner of the infirmary, watching the hustle and bustle as the medical staff dressed in protective clothing treated their patients and collected blood from all of those who had been present in Tower 3. Her eyes were repeatedly drawn to one particular area that was hidden by a drawn curtain.

Finally, there was movement there as the curtain was shifted just enough to allow Carson to exit with a weary sigh.

Carson,” she called quietly to get his attention. He quickly joined her. “How are they?”

I've put Colonel Sheppard in a medically induced coma for now. I was afraid he might break through the restraints. As for Rodney, well the news isnae very good.” He sighed again. “The retrovirus saved his life as the wound he suffered would have been fatal otherwise. However, it is speeding through and mutating his system even faster than the Colonel’s as evidenced by how quickly his body is showing the physical signs. It took nearly a full day for the Colonel to start showing any physical symptoms but it’s been less than two hours since Rodney was infected.” He shook his head. “I immediately started him on the viral inhibitor and I’ve sedated him as he was getting increasingly frantic, even for Rodney. But as you know it won’t help much.”

Elizabeth frowned. “Why is it affecting Rodney so much faster?”

There could be any number of reasons. Don’t forget this was all experimental and it wasn’t ready.” He shook his head. “But if I had to guess there are three reasons that I think are the most likely, or even a combination of the three. One, Rodney received a strain of the retrovirus that has already torn through the Colonel’s body and immune system. Two, Rodney was infected through a wound in his chest, close to his heart, which pumped the infected blood throughout his body much faster.”

And the third?” Elizabeth prompted when Carson trailed off.

The ATA gene therapy. Rodney’s DNA has already been changed with a retrovirus in order to give him the ATA gene. Then there is the fact that the original gene therapy that Rodney received was based on Colonel Sheppard’s gene, in essence giving him a small bit of the Colonel’s DNA and it was the Colonel’s infected blood that Rodney was exposed to the retrovirus through...” he trailed off, spreading his arms helplessly. “The only good news is that no one else was exposed to the retrovirus. It seems to need direct blood to blood contact in order to spread.” He gestured to where the rest of the medical staff were ushering everyone to another part of the infirmary. “We’re going to restrict access to this section of the infirmary to prevent anyone else being accidentally exposed.”

Elizabeth breathed a sigh of relief at that bit of good news. But her eyes were drawn back to the curtained off area. “So, what now?”

Carson shook his head wearily. “The retrovirus has wreaked havoc on their systems, and it's taking over.”

What does that mean?”

It means if we don't find a way to stop the retrovirus in the next 24 hours, what is left of the John Sheppard we know will be gone. And Rodney won’t be far behind.”

Elizabeth’s heart clenched at his chilling words. It was looking very likely that she would lose two good men, two good friends.

Carson must have seen something in her face because he tried to reassure her. “I’m nae giving up yet. I’m going to do everything I can to save them.”

Elizabeth nodded, schooling her face. “Keep me informed. I have to check in with Hermiod on the Daedalus. He thinks he can use the transporter beams to get the Goa’uld out of Colonel Caldwell. And that’s another thing to be grateful for, he appears to be the only one to have been compromised.” She patted Carson on the arm and, with one last look at the curtain concealing Sheppard and McKay, she made her way to the infirmary exit. She had some people to talk to, bad news to spread. Unfortunately, it might be time to start saying some goodbyes.


Carson stared after Elizabeth for a long moment before shaking his head and heading to his office. He sat and pulled up the lab results for the two men and compared them to their original files. He sat there for several long moments trying to think of a way to reverse or at least halt the process. But the fact remained that his ‘magic bullet’ idea was their only hope and without the Iratus stem cells there was no chance of it working. He sighed and climbed back to his feet, heading back to the curtained-off section of the infirmary.

He could not help wincing at the sight of the spreading blue scales across Rodney’s body beneath the scrubs he wore. His chest was fully covered with them, what with it being the initial infection site. His arms, restrained as a precaution, were also partway transformed at this point as, as was his neck, with scales starting to creep up his face.

A blue eye cracked open suddenly, the color the same but the pupil now slit like a cat’s. “Carson?” Rodney croaked out, his nostrils flaring slightly.

Aye Rodney, it’s me. How are you feeling?”

Everything’s fuzzy. Why am I in the infirmary?” He tried to move his hands but was halted by the restraints. “What? Why am I restrained?” His eyes widened at the sight of the blue scales covering his arms. “Oh my God.” He began jerking in his restraints as his heart monitor began to blare an alarm at the increased heart rate.

Rodney! Stop, you need to calm down lad!” Carson tried to talk him out of his panic. “The increased heart rate and adrenaline will only speed up the retrovirus.” But his words were having no effect and with a sigh he retrieved a prepped syringe from a nearby table and injected its contents into Rodney’s attached IV.

Within moments the astrophysicist began to calm. “Carson, what...” His voice trailed off as the sedative did its job, once more putting the scientist to sleep.

Even as the tension eased in the Canadian scientist it increased in the Scottish doctor. He felt like the weight of the world was on his shoulders. “I’m so sorry lads. This is all my fault. I wish I’d never created this bloody retrovirus.” Carson wanted to punch or throw something but he knew it would solve nothing. He glanced over at Colonel Sheppard but of course the man hadn’t awakened.

Sheppard’s nostrils flared as if scenting the air, an action reminiscent of Rodney’s own as he woke up. Carson stepped closer, checking the various displays just to be sure the man remained in his medically-induced coma. The nostrils flared again, but Sheppard showed no other sign of regaining consciousness.

I wonder how sensitive your sense of smell has become,” Carson murmured thoughtfully. “Both of ye seem to be scenting the air unconsciously.” He recalled Sheppard’s words about Caldwell smelling wrong. “You seemed to be able to smell the symbiote in Colonel Caldwell. I wonder was it the symbiote you were smelling or a chemical change in the host body due to the release of-” Carson stopped himself mid-sentence, his eyes widening as his thoughts sparked an idea.

Of course! The Iratus bugs use scent to identify predators, prey and their own kind. To communicate with one another.” He strode over to a cabinet and retrieved a sample kit. Opening it, he swabbed Colonel Sheppard’s neck where the sweat glands were located. “Please let me be right,” he muttered as he hurried over to a device that they had discovered analyzed samples and compared them to the database. He placed the swab inside it and waited.

Thank God,” he muttered a short time later, though it felt much longer, when the analysis was complete and the results were displayed. Keying his radio, hope began to fill him. There might just be a chance after all. “Dr Weir, I need to speak to you immediately.”

What is it?”

Meet me in your office. I think I have an idea.” He ended the transmission and glanced back at the two unconscious men. “Hold on lads,” he murmured before hurrying toward the infirmary exit and the nearby transporter.

He arrived at Elizabeth’s office and entered it. Moments later she hurried in, followed by Teyla and Ronon.

I'm sorry. It just came to me. The fact that Colonel Sheppard’s mutation has progressed as far as it has may be his and Rodney’s salvation.”

Explain that,” Elizabeth ordered.

His sweat glands are actually producing trace amounts of their signature pheromone,” Carson said as if it explained everything since for him it did.

And?” Elizabeth asked while Teyla and Ronon looked confused.

And his sense of smell has increased drastically. He was able to smell the symbiote in Colonel Caldwell, or rather the pheromones it released into his body,” Carson continued excitedly.

Okay, but how does this help us?”

Don’t you see? The Iratus communicate through scent. When we were in the cave, those bugs knew we didn't belong there. So they didn't really fancy us getting close to their nest.”

Elizabeth nodded as that information sunk in. But it was obvious she still didn’t know how it helped them.

Teyla frowned in confusion as she tried to work through to what Carson was suggesting. “Since Colonel Sheppard is producing this pheromone does that mean you are able to reproduce it?”

Carson’s face fell. They weren’t catching on. “Aye, we could,” he answered.

Elizabeth’s face lit up. “That’s an excellent plan, Carson.”

He shook his head. “I wish it was.”

You can’t do it in time?” Ronon asked.

No, it would take days.”

But you said Sheppard only had 24 hours before the damage the retrovirus is causing would be irreparable. And Rodney not much longer than that.” Elizabeth frowned.

Exactly.” Carson waited for them to get it.

Surprisingly, or perhaps not, it was Ronon who got it first. “You want Sheppard to go.”

Aye. He’s the only person who wouldn’t need an artificial pheromone. He could walk right into that cave, and those bugs wouldn't pay him any mind.”

But Elizabeth was slowly shaking her head. “I’m not sure that’s such a good idea, Carson. He’s not exactly in his right mind at the moment. You saw how he was acting. Could Rodney go instead?”

While Rodney’s mutation is spreading quickly he isnae yet producing the pheromone. And even if he were I wouldn’t recommend sending him. We’ve been keeping him sedated because each time he wakes and sees how far the transformation has spread he panics which causes his heart rate to increase and adrenaline to flood his system, which only speeds up the retrovirus’ effects. Not a good idea.” Carson shook his head. “As for Colonel Sheppard, well he didn’t try to hurt anyone except in self-defense. And he stopped taking the inhibitor we were administering. It was able to keep him lucid.”

I thought its effectiveness had worn off?” Elizabeth asked.

True, but I believe if we give him a massive dose, he may be clear-headed enough to complete the mission before we lose him completely.”

As I understand it, would that not be dangerous?” Teyla questioned.

Aye, it’s dangerous. It could possibly kill him. But even if I knew it would for certain, I'd be tempted to offer him one last hour of lucidity.”

Elizabeth frowned, obviously considering all of the information. Carson held his breath. Finally, she nodded at him. “Do it.” She looked at Teyla and Ronon. “Gear up. Take him as far as the cave.”

They nodded and turned to exit.

Wait.” When they turned to look at her she continued. “Nobody tell him about Rodney being infected. He doesn’t need to be worrying about that on top of everything else.”

Ronon frowned. “That’s stupid. He’ll try harder to succeed if he knows it’s for McKay as well as himself.” Teyla also appeared troubled.

I mean it. I don’t want him worrying about Rodney instead of his task.” Elizabeth’s tone was firm and final.

Whatever,” Ronon huffed out. “Can we go already?”

She nodded and they left.

Let’s go, Carson, you have a patient to wake.”


John’s eyes snapped open and he gazed at the ceiling. Infirmary, he was in the infirmary again. But the last thing he remembered was being in his quarters, Elizabeth speaking to him. Then things got fuzzy. Everything after that was a blur.

John? John?”

Speak of the devil. He turned his head to meet her gaze, spotting Carson standing beside her.

Hey,” she smiled. You’re in the infirmary.”

Obviously, he thought but didn’t comment. His throat felt weird, would he even still be able to speak?

Sorry about the headache. It's a side effect of the inhibitor.”

Like he cared about that. “Did I hurt anyone?” he managed to rasp out. Hey, look at that. He was still capable of speech, though it felt weird.

No, not seriously,” Elizabeth tried to reassure him.

But John wasn’t sure he believed her. He was having trouble remembering but he was sure someone had been hurt, and badly at that. An image of blood gushing beneath his hands flashed briefly through his mind and he flinched away from it. Looking at Elizabeth and Beckett, he decided not to ask just yet, positive that they wouldn’t answer honestly. Instead, he asked something else that was on his mind. “Did Ronon shoot me?” That was something else he thought he remembered. ‘Too bad his gun was set for stun,’ he thought darkly.

You had it coming,” Elizabeth answered with a wry smile. “Look, we don't have a lot of time. This dose of the inhibitor drug will only last about an hour. How would you like to go on a mission?”

His attention focused sharply on her at that. What kind of mission could he go on like this? He listened as they explained and when they were done he gave a sharp nod of agreement.

A short time later found him entering the gate room, a hooded cloak hiding the worst of the mutations from view. He frowned as he saw Teyla and Ronon waiting by the active stargate, alone. Where was McKay? He thought about that image of gushing blood. Had he - - ? No, he couldn’t have, that didn’t feel right when he thought about it and surely someone would have told him if he had attacked Rodney.

But still, where could he be? Unless he didn’t want to face what John had become? After all, Beckett’s idea seemed like a long shot. Rodney probably didn’t want to see the monster John had become. Despite not wanting Rodney to see him like this either, the idea that Rodney didn’t want to see him hurt.

He brushed those thoughts aside as Beckett hurried them through the gate.

It was a long but brisk walk through the forest on the other side, made in silence. John concentrated on keeping hold of himself. Even now he could feel the inhibitor wearing off but he was not giving up his mind without a fight.

Finally, they reached the cave. Beckett held out a large thermos-sized container. “Use this, and collect as many as you can. Oh, God. At least a container full. Do you understand?”

John looked at it. What was the point? He could feel himself slipping away already. Like this was really going to work.

Colonel, do ye understand?” Carson repeated, his voice and scent full of worry.

His scent?’ John thought in confusion.

Sheppard.” He turned to face Ronon who wore a defiant look. “I’m sure you noticed the lack of McKay’s whining.” Now Ronon had John’s complete attention.

Ronon,” Teyla said warningly.

He ignored her. “The reason he’s not here is cause he got infected too.”

John’s eyes widened at that. Oh God, had he attacked McKay after all?

He must have made a sound or shown some type of reaction because Carson hastened to reassure him. “Wasn’t your fault lad, you were actually protecting him when you both were injured and your blood got into his wound.”

John wouldn’t have believed him except he could smell the truthfulness of that statement. And what was up with that?

So you need to get those eggs for McKay’s sake too,” Ronon added.

John nodded and reached for the container. He wished they had told him before. How much time had they wasted while Rodney was suffering the same fate as him? He would do whatever it took to give Rodney a fighting chance.

Colonel Sheppard? You know that we cannot go in there with you, but you need to hurry. It took us a little longer to get here than we would have liked.”

John heard Teyla’s words but didn’t acknowledge them as he walked into the cave. He had a mission to complete. He hurried through the cave and soon reached the cavern they had told him about. He removed the robe and pulled out a flare, activating it and tossing it into the cave. ‘That’s a lot of bugs,’ he thought but they weren’t going to stop him. He noticed the two desiccated corpses nearby but didn’t have time to do anything for them. He had other priorities. He strode forward before leaping up onto one of the nests and shoving his arm inside. He quickly began to fill up the container.

When the container was about three-quarters of the way full John felt his lucidity slipping away. ‘No!’ he thought. ‘Beckett said a full container, I am not going to fail Rodney.’ He held firm to that thought as he continued to fill up the container. Finally, he finished and, releasing his hold on the nest, he jumped down to the ground and sealed the container. A wave of pain swept over him as he felt the last of the inhibitor leaving his system. No, he wasn’t done yet. He had to get this to Beckett for Rodney’s sake. Rodney was depending on these eggs.

John held firm to that thought as he forced himself to his feet and began to run toward the cave entrance, keeping a firm grasp on the container. He could not lose it. There! The cave entrance came into view. ‘Got to get eggs to Rodney, got to get eggs to Rodney.’ The thought repeated over and over in his mind as he continued to run. That was his only focus as he burst out of the cave, paying absolutely no mind to his surroundings. Then there was a high pitched whine, a brief burst of pain and then only darkness.

Chapter Text

It was the beeping that caught his attention first, followed by that antiseptic scent that told him he was once again in the infirmary. John’s eyes remained closed as he tried to recall just what had landed him there this time.

And then memory returned and his eyes snapped open as he tried to jerk upright only to be stopped by the restraints holding him to the bed.

Easy lad, you’re alright,” Beckett hurried over to his side, assurances falling from his lips.

John stilled his thrashing about. “Did it work?” he asked, though a quick look at his arms showed they were still covered in blue scales. But just the fact that he was in possession of his own mind told him that something must have worked.

It is working,” Carson confirmed. “Your brain scans are already returning to normal. And we’ve seen some reversal in the retrovirus’ effects. For example, you may notice that you’re having an easier time speaking. Your vocal cords are in the process of reverting. It appears that the inner changes are reversing themselves first. I’m sure the rest of the changes will follow suit. Granted it won’t be overnight but I believe you should be back to yourself in a relatively short time.” He patted him on the shoulder.

Then are these really necessary?” John asked as he pulled on the restraints. “And where are we anyway?” he asked as he looked around, not recognizing the room they were in. It was much smaller than the infirmary, made even smaller by the curtain blocking off part of the room.

Sorry lad, it’s just a precaution until we’re sure the retrovirus is completely out of your system. As for where we are, it’s a small room off the infirmary we believe was used for those needing longer-term treatments. We haven’t needed to use it before now but figured you lads could do with a bit of privacy you won’t get in the main infirmary while you recover.”

Carson’s words reminded John of what he had learned outside of the cave. “McKay!” He began struggling again, needing to reassure himself that the scientist was fine.

What?!” Came the aggrieved response from beyond the curtain. “First they won’t give me a laptop to do any work and now I can’t even sleep with all of the commotion in here. Not that anyone could sleep on this pathetic excuse for a mattress. I have a bad back you know!”

John’s struggles ceased and he felt himself relax slightly. McKay didn’t sound hurt. In fact, he sounded like his normal, grouchy self.

As you can hear Rodney is feeling like his old self again as well,” Carson said with a fond but exasperated look at the curtain.

And what is that supposed to mean?”

I think you know exactly what I meant ye bloody pain in-”

Since you’re awake anyway we might as well get rid of the curtain,” John interrupted Carson. As much as he loved McKay baiting, it was more fun if you could see his expressions. Plus, John wanted to see with his own eyes that his scientist was alright. He paused at that thought. His? Since when was he so possessive over the Canadian genius?

As he pondered that thought he almost missed said genius’ protest. “What? No! There is no need to move the curtain, it’s fine where it is!”

John eyed the curtain suspiciously. What was McKay trying to hide?

Carson leaned toward John and winked. “Don’t take it personally lad, Rodney’s being a bit shy about anyone seeing him in his current state,” he told him in a stage whisper.

I am not being shy! I just don’t want everyone gawking at me like I’m the main attraction in a freak show!”

John could understand that, as he himself had hidden in his room as the changes progressed. But still-

Come on McKay, it’s just me and Carson. He’s obviously already seen you and you can’t look any worse than I do, you weren’t infected anywhere near as long as I was.”

Carson’s flinch and the utter silence from the other side of the curtain made him doubt his own words. “McKay? Rodney? Come on, it can’t be that bad. Look, I’m the only one who knows what you’re going through, I’m not going to make fun of you.”

Carson cleared his throat. “While it’s true that Rodney was not infected as long as you were Colonel, the retrovirus sped through his system much faster than it did yours.”

John looked down at his arms and the blue scales there, the odd spiked protrusion growing here and there, the fingers tipped in claws. Guilt filled him as he wondered just how much further Rodney’s changes had progressed. He was the one who had infected Rodney after all.

Oh, go ahead and open the curtain Carson,” Rodney groused.

Carson did so and then looked between the two of them. “Well, I’ve got to go check in with the main infirmary. Just hit your buttons if you need anything.” With that he left the room, escaping the awkward silence that had filled it.

Well?” Rodney asked once Carson had gone.

Slowly John lifted his gaze from his hands and turned to look across the room, taking in the changes that had taken over his friend. His lower body was covered by a blanket but John could make out some odd bumps that spoke of protrusions similar to the spikes he himself now had, mainly near the joints of his knees and ankles. His eyes next landed on the arms, laid bare to sight by the hospital scrubs, now similarly scaled like his own. Again, spiked protrusions were visible from the elbows. John’s newly enhanced eyesight caught the faintest trace of the scar on Rodney’s arm. Too bad the retrovirus couldn’t completely remove the reminder of Kolya, and instead simply made it harder to see. John would have preferred it if the painful reminder could have been completely erased. After a moment, he let his gaze continue to take in the rest of Rodney’s changes. Thicker scales covered the vulnerable wrists, while only a light smattering spread across the palms and back of hands to the clawed fingers. John blinked in surprise, were those extra joints in the fingers? He glanced back at his own fingers but no, that was not a change he himself had experienced.

Returning his gaze to his strangely quiet friend, he glanced at his chest. Though covered by the scrubs he could see hints of the thick scales peeking through the opening. Like his own chest, they were thick, almost like armor. Trailing up to the neck, the thickness continued around the vulnerable neck before thinning out as it spread across Rodney’s lower face, his jaw and cheeks, though his nose and the center of his forehead remained clear. His ears were tinted blue, though there were no actual scales. He allowed his gaze to trail higher, where a single blue patch tinted each of the temples, tiny blue spots trailing along the edge of his receding hairline.

John swallowed and gathered his courage before allowing his eyes to finally meet Rodney’s.

The bluest eyes he had ever seen remained the same, save that the pupils were now slit like a cat’s, a change similar to one he had seen in his own before he had shattered the mirror to remove that image.

I look horrible, don’t I? Carson wouldn’t let me see but I can see my own arms and feel the itching across my whole body. I’m hideous! This is why I didn’t want anyone to see me,” Rodney blurted out as he tried to move his arms to cover himself only to be halted by the restraints.

No!” John denied, a bit more forcefully than intended. “You look fine,” he added lamely.

McKay gave him a skeptical look and he continued. “You’re still you, just a bit more...” he trailed off, unsure how to continue.

What? Scaly? Blue?” Rodney rolled his eyes. “Please. Can you honestly say you feel the same way about yourself and then tell me I look okay?”

John had to concede his point. He himself was not fine with the changes his body had gone through. “Well, it’s not like we have to worry about staying like this. Beckett said the cure was working.”

Yeah, if Carson’s right about his voodoo. You know it’s not a real science,” McKay grumbled.

John eyed him. “How did you get infected anyway? Beckett said something about my blood getting into your wound? How did that happen? Did I-?” He couldn’t finish the question.

What? No!” Rodney looked startled. “You don’t remember?”

Last thing I remember for sure is being in my quarters with Elizabeth. Then I woke up in the infirmary before they sent me to the cave. Everything in between is a blur.”

Huh. Well, my being injured wasn’t your fault,” Rodney started to say before stopping and glaring at John. “Unless you count your suicidal tendencies.”

My what?” What the hell was McKay going on about now?

If Rodney could burn holes into a person with his glare alone, John would be swiss cheese.

Oh please, genius here. You think I didn’t put it together? You didn’t hurt anyone more than bruises but you did attack several of the search teams in order to get them to shoot you, granted with stunners, and then you headed for an empty, isolated area of Atlantis where the soldiers would have no problem finding you. Plus I heard about what you said to Elizabeth, that if she wouldn’t send more men after the eggs that we might as well kill you now. You were trying to get them to kill you!”

His voice had steadily rose and was punctuated by his heart monitor blaring an alarm.

Carson hurried into the room. “What’s going on in here? Rodney, you know you need to keep calm or I’ll have to sedate you again.”

Tell that to Colonel Suicidal over there,” Rodney grumbled as he took some deep breaths to try to calm down.

I wasn’t trying to kill myself, at least not consciously,” John defended himself. “I told you, I don’t remember.”

Convenient,” Rodney huffed before settling down at Carson’s look.

Are ye two talking about Colonel Sheppard’s little breakout?” Carson asked. At their nods, he shook his head. “I don’t believe the Colonel was trying to kill himself. Actually, based on the behavior I observed from the footage of his interaction with you Rodney, I believe the Colonel was trying to find and deal with a threat.”

What threat?” John asked, trying to remember. He thought back to being in his quarters and tried to remember what happened after. He paled as an image of his hand around Elizabeth’s throat flashed in his mind. “Did I attack Elizabeth?”

I’m afraid so, but you only bruised her before releasing her. I’ve got a theory about why.”

Yeah, this threat you think I was looking for. What threat did I find in Elizabeth?” John asked, disgusted with himself for his own actions. First Rodney, now Elizabeth. Who else did he hurt while out of control?

Your sense of smell was heightened by the mutation you’ve been undergoing. Elizabeth had been spending a lot of time with Colonel Caldwell. I believe you smelled the pheromones released by the Goa’uld symbiote that she was exposed to,” Carson explained.

Both John’s and Rodney’s eyes widened at the news and they tried to speak at once.

Wait, what?!”

A Goa'uld?! Here? How the hell did that happen?”

Carson looked like he wanted to slap himself in the forehead. “Aye, that’s right. I forgot neither of you were conscious for that little discovery.” He sighed. “Well, it was after Rodney was injured and Caldwell found the three of us-”

Wait,” John interrupted. “I still don’t know how Rodney was injured. And what were you doing there Carson?” If it was an unoccupied section of Atlantis like Rodney said earlier then there was no reason either of the two should have been there with John on the loose.

Rodney sighed in a put-upon manner. “You have to start from the beginning Carson, or he’ll just keep interrupting. It started with us in the control room, or more specifically me, programming the sensors to track you.” It was obvious Rodney wanted to know what had happened from when he lost consciousness but was willing to, not so patiently, fill John in up until that point.

John listened, partly in disbelief, as Rodney detailed his decision to seek John out on his own, unarmed: how he got hurt trying to protect John. His disbelief was rapidly turning to anger as he continued to listen. Finally, they got to the point where McKay lost consciousness from his injury and Carson took over the explanation up until the point where John first woke up in the infirmary before being sent to the bug planet.

And you know the rest from that point,” Carson finished before finally registering the dark look being sent McKay’s way by the military man. “Er, I believe I’ll leave you two to discuss this in private, I have rounds to do.” He made a hasty exit.

The door had barely shut behind him before John was speaking, unable to keep silent any longer. “What the hell were you thinking?!”

Rodney gaped at him for a moment before drawing himself up as much as the restraints allowed. “Aren’t you the one always going on about no man left behind? I was thinking that I was saving your life, though now I wonder why I bothered,” he shot back. “Some people just don’t know how to be grateful.”

Oh, and you think I should be grateful that you stupidly risked your life? You had no way of knowing how I would react, I’d already attacked Elizabeth and several of my men! Damn it, Rodney! It could have easily been me who put you in that hospital bed! You had no way of knowing I wouldn’t attack you!” John knew he shouldn’t but the words came pouring out, despite his best efforts to stop them. “And you wonder why I have trouble trusting you since Doranda?”

Rodney visibly flinched back at the words, his mouth closing with a snap as he averted his eyes. But not before John saw the hurt in them.

Shit.’ He knew he shouldn’t have mentioned Doranda but he was so pissed at McKay putting himself needlessly in jeopardy, again . He was trying to think up an apology that wouldn’t back down from his original point when Rodney’s soft-spoken reply barely reached his ears.

I couldn’t let them kill you.” Rodney still wasn’t meeting his eyes. “What would you have me do, stand aside and just let them kill you?”

John swallowed but answered. “Yes.” Yes, if it meant keeping Rodney safe then that was exactly what he should do.

Rodney finally lifted his gaze to meet John’s, whose heart began to speed up at the emotion visible there. “I can’t do that. Not when it’s you.” He swallowed nervously, visibly gathering his courage. “I am sorry about Doranda. I know that I said it was about the Nobel but it wasn’t. Oh, that would have been a bonus but it wasn’t my real motivation. If I could have done it, it would have given us unlimited power. We wouldn’t have to worry about the shield losing power if there was another siege. And the weapon, if I could have gotten the weapon to work we would never have to worry about the Wraith again.” His gaze dropped to the blanket and his voice grew quieter. “You wouldn’t have to fly another suicide mission.” His voice dropped to such a bare whisper that if it wasn’t for John’s enhanced hearing he would have missed the next statement. “I really thought I could do it, I never would have risked your life like that if I had any doubts.”

Now John really felt like the worst piece of shit ever. “Rodney-”

Don’t,” he said, stiffening as he turned his head away. “I’ll understand if you want me off the team.”

It was never that you risked my life with Doranda, it was that you risked your own.” The words came out almost unconsciously as John kept seeing that unnamed emotion in Rodney’s eyes. Normally John would have clammed up. But the mention of leaving the team, that was something John had to fix and this was the only way. And after Rodney’s honesty, it was only right that John do the same.


John licked his lips nervously. “You’re too important. I have to keep you safe.” He forcibly relaxed his face, letting the mask he usually wore slip away, silently pleading with Rodney to understand.

You- Oh.” Rodney’s eyes widened as he stared at John’s face, a look of incredulous wonder crossing his face. “Really?” he asked hopefully, as his face flushed a darker blue.

John swallowed but nodded as his throat closed up, unable to verbalize his emotions further.

Suddenly Rodney was grabbing the call button near his hand and repeatedly pressing it.

Carson! Carson! Come on, I need these restraints removed! And bring me a laptop, there’s work that needs to be done before some idiot sinks or blows up the city!” But the look he shot John told him that wasn’t the real reason he wanted the restraints removed.

John gave him a small grin, then settled back to watch the show as an irritated Carson appeared in the doorway to argue with the astrophysicist.


Rodney scowled down at his computer screen, seriously considering hacking into the medical records. Would it really be wrong if it was his own records? He had a right to that information!

Don’t,” Sheppard said from where he was pacing back and forth across the room, obviously restless from their week long confinement. Though thankfully the restraints had been removed after that first day. Sadly, they had both agreed that any change in their relationship would have to wait until they were released. The room, while private, was being monitored and it was too big a risk to take. Thus, a week of boredom had ensued.

Come on, you know they’re hiding something from us! It’s our bodies, we have a right to know.” Despite Carson’s assurances, there had been no sign that the visible mutations were reversing themselves, and each day his explanations grew weaker and weaker, with him telling them to be patient and give it more time.

You think I don’t know that?” Sheppard stopped his pacing to run a hand through his disheveled hair. “But if you hack into the files they’ll know.” He held up a hand to ward off Rodney’s protests. “I know, I know, you’re smart enough not to get caught. But if we suddenly have the information they don’t want us to have then even without the evidence they’ll know. And that’s a risk we can’t afford to take right now.” He resumed his pacing.

Rodney frowned. “What? Why would it be a risk? I mean they might get irritated but they have to know what would happen if they didn’t share the information.”

John made a noise of frustration. “Look, it’s obvious to both of us that we’re not changing back, right?” At Rodney’s nod, he continued. “What do you think the SGC’s going to do? Let us stay in charge of our departments? The only reason we weren’t sent back to Earth for ‘debriefing’ when the SGC summoned Caldwell back is because we were undergoing a treatment that appeared to be working at the time. That’s no longer the case.”

Rodney swallowed back his protests as he considered John’s reasoning. While Hermiod’s hare-brained plan to use the Daedalus’ transporters to remove the symbiote from Caldwell had worked, when the details had been reported to the SGC in a scheduled transmission, they had replied with orders to immediately send Caldwell through the gate back to Earth while his second in command brought the Daedalus back. Rodney could kind of see the point, Caldwell no doubt had valuable information from the Goa’uld to impart. But why would they want John and Rodney back? Unless-

You think they would dissect us? Experiment to see how the retrovirus has changed us?”

Rodney began to panic, thinking of all of the fates that might await them on Earth. He was already sick of all the testing they had been put through this last week to discover what changes their bodies had undergone. And oh, had there been changes. But Rodney had gotten through it by telling himself that they were being cured so it wouldn’t matter in the long run. He had heard some of the medical researchers commenting with curiosity on some of those changes and how they would like to study them further when they didn’t think he could hear, his enhanced hearing being one of the said changes. And if that was from people who knew him and Sheppard personally, if not well, then how would strangers react?

Hey, calm down it’s going to be alright,” John tried to soothe him, coming over to place a hand on his shoulder and give it a tight squeeze. “Elizabeth would do everything in her power to keep that from happening.”

Rodney latched onto that statement. “That’s right, she wouldn’t let that happen. So what are you worried about?” He began to calm down.

That means that we can’t do anything to jeopardize her position. We’re already viewed as compromised, so if you do something like hacking into the medical records they could use that as an excuse.”

Oh. Then what are we supposed to do, just sit here twiddling our thumbs?”

But before John could answer the door opened and a grim looking Carson entered. “Good morning lads,” he greeted weakly.

Rodney had had enough. “Carson, would you please just tell us what is going on? It’s obvious the treatment isn’t working and that you’re hiding something from us. We’re going crazy here imagining the worst possible outcome.”

Carson sighed, his whole body posture reflecting his weariness. “I’m sorry lads but the treatment isn’t working any longer.”

You said that things were reverting back to normal. So what changed?” John asked, his eyes narrowed.

The retrovirus ran its course through your system. You no longer have any trace of it in your bodies,” the doctor started to explain.

No trace?! Then what do you call this?” Rodney asked as he gestured with his hands at him and John.

You have to understand, the retrovirus acted as a catalyst, using the Iratus DNA to change you at a genetic level, which is what caused your mutations. We injected your original DNA back into your bodies in order to reverse those changes, using the Iratus stem cells to carry it along the path of the retrovirus.”

But you said the retrovirus is gone,” John pointed out.


So why not just inject us with more of our own DNA?”

Without the retrovirus acting as a catalyst, there is nothing to trigger the change.” He held up a hand to forestall them. “And before you suggest it, exposing you to more of the retrovirus is not an option. We ran simulations and exposed some of the samples we have taken from you to it. Each time the effects were different, unpredictable.” He sighed again. “I’m sorry lads. I know this isn’t good news.”

Not good news? It’s horrible news! Look at us! The only way we’ll be able to return to Earth is if they locked us up.” Rodney’s hands were flying through the air as he spoke.

We’re not giving up lads, I promise ye that. I won’t give up until I’ve figured something out.”

There’s nothing else?” John asked.

Carson shook his head. “This ‘magic bullet’ idea was our best hope. We have some ideas that we’re working on but,” he hesitated then continued, “while we think we might eventually be able to treat the Colonel in a way to make the effects less visible, I’m afraid we can’t say the same for Rodney, at least not at the moment.”

What? Why?”

Despite your shorter time of exposure, the retrovirus wreaked more havoc on your system. And your body has been through so many genetic changes, what with the gene therapy, the retrovirus and our attempt at a cure, that we believe any further changes will irrevocably destabilize your DNA. In other words, it could cause your body to start breaking down.”

Rodney sat heavily on his cot as the words sunk in. He would never return to normal.


All eyes turned to John as his firm denial.

John?” Rodney asked.

But John was staring at Carson. “You want to keep working on a treatment, then fine. But I will refuse to take it unless it works on both of us. You fix both of us or neither.”

Rodney stared at him. “You can’t-”

John cut him off, turning his resolute gaze on the scientist. “I don’t leave people behind. Whether the enemy is the Wraith, the Genii, or the effects of a mutation.” His gaze softened minutely. “I’m not leaving you to face this by yourself.”

Rodney found himself speechless.

Colonel, I urge you to reconsider-”

John cut Carson off too. “Both of us or neither,” he repeated.

Carson nodded. “Like I said, we will keep working on it. But for now, there’s really no point in keeping you here. So I will be releasing you to your own quarters.”

And probably confined there if John’s theory was correct. So instead of staring at the walls of this room, he would be staring at the walls of his quarters. Granted, on the one hand there were more things to distract him from his thoughts there. But on the other hand, no John to talk to. And after John’s bombshell decision they really needed to talk.

John, however, was already nodding at Carson’s words, obviously relieved to be released. “Any idea on the SGC’s reaction?”

Carson shook his head. “No clue. And if Elizabeth has an inkling she’s not saying.”

Just wonderful, something else for him to worry about to death while stuck in his quarters.

I’ll just call for your escort, shall I?” Carson said as he made his retreat. Because of course they couldn’t be allowed to wander the city alone.

Alone again, Rodney got up from his cot and took a step closer to John. “John.”


If it were me they could treat instead of you, you’d be telling me, no, ordering me to take it,” he pointed out.

Beckett said they have ideas that might possibly work for me. That’s not definite. And until it’s something they’re sure will work for us both then they can keep trying but I don’t have to be their guinea pig.” He scowled darkly. “Once was enough.”

But if they could reverse the changes, you could find someone. Someone better.”

Better than you?” he asked, stepping closer, crowding Rodney up against the wall. “I already have someone. Unless you’ve changed your mind?” he questioned hesitantly. “If you don’t want me like this?” He gestured to his body.

No! I just, I can’t - - ,” Rodney couldn’t find the words.

Despite your confidence when it comes to your work, you can’t believe anyone would really want you,” John finished for him.

Exactly. Especially now. I know I wasn’t much to look at before, especially compared to you but now.” Rodney gestured to his own body in explanation.

Well, I always thought you looked good. If you can accept me looking like this then why would I have a problem with you looking like that? And I’ve told you before, I think you look fine.”

Rodney watched as John’s cheeks flushed a darker blue. “I- Thanks. I think you look good too,” he said, feeling his own cheeks flush. Embarrassed, he started speaking, needing to fill the silence. “It’s probably the pheromones Carson was talking about. After all, we’re the only ones of our kind, it’s not outrageous to believe that’s what is causing the attraction.”

Rodney!” John said with fond exasperation evident in his voice. “Shut up.” He lifted a hand to rest on Rodney’s cheek. “It’s not the pheromones.”

You can’t know that.”

John shook his head, amusement visible on his face as he leaned in. “Trust me, I can.”

What? Oh,” Rodney said as his meaning sunk in, followed by recognition of the meaning of John’s actions. His eyes started to close as he leaned forward to meet John halfway.

But before their lips could touch a noise from outside drew their attention and they separated moments before the door opened, revealing their Marine escorts.

Damn it! So close. Rodney shared a frustrated look with John, then stepped closer to the Marines who were not meeting their gazes. “Well, it’s about time. What took you so long? I’m sick of this place and want to get back to my quarters to rest. Well? What are you waiting for? Chop, chop.”

He had so many things to consider. But first thing’s first, a shower was needed. Possibly a cold one.

Chapter Text

John strode quickly through the corridors toward Elizabeth’s office, his Marine escort trailing behind. He tried his best to ignore the stares of the personnel they passed but the whispers continued to reach his enhanced ears. He would swear he could smell their pity.

Still, it was good to finally be out of his quarters. He’d been going crazy stuck in there the last week and a half. And the infirmary before that. At least in the infirmary he’d had McKay’s company. In his quarters he’d only been able to interact with the men who delivered his meals and they didn’t tend to stick around. He’d had no way to release his pent up energy, nothing to really relieve his boredom. He’d been climbing the walls, literally. It had been a relief when the summons to Elizabeth’s office had come. Despite the uncertainty of what would come from this meeting at least something was finally happening. And just in time, he’d been considering climbing out his window and seeing how easy it would be to climb the outside of the tower which would not have done his precarious situation any good.

John was just glad that something was finally happening with regard to his situation. He’d found himself becoming angry the longer the situation lasted. He and Rodney were the victims and yet it felt like they were being punished for circumstances beyond their control. Neither of them had asked for this to happen to them but it did. Now not only were they paying the price for others’ mistakes, but they were being punished for it too.

Damn, he had to change his line of thinking. It wouldn’t do to go into the meeting in a temper. It could make things worse. First, he had to find out what had been decided for him and Rodney.

Speaking of, John spotted Rodney up ahead with his own escort and increased his pace to catch up. “Hey,” he said, giving him a quick look over and finding him none the worse for wear. Relief filled him at that. He hadn’t realized until this moment how much of his tension was due to the lack of contact with Rodney. “How you doing, buddy?” He stepped closer to bump their shoulders together.

Hmm, as well as could be expected. Considering I haven’t been allowed access to the labs and have had to monitor everything I could from a single laptop. Who knows what kind of shoddy work has been happening. It’s a wonder the city is still standing.”

John couldn’t help a quick grin. Same old McKay, just different packaging.

Well, it’s nice to see that some things are still the same,” Elizabeth commented with a strained smile as they entered her office, obviously having heard Rodney’s comment.

John noted with relief that the glass wall he had damaged had been repaired. Elizabeth gestured them inside while motioning for their escorts to remain outside and shut the door. Rodney immediately began speaking. “Do you have any idea how far behind I am in my work? How long is this confinement going to last?”

Gentlemen, please sit down.” Elizabeth gestured to the two seats in front of her desk, her entire posture exuding weariness.

Elizabeth?” John asked as he and Rodney sat down. He immediately slouched in the chair, earning a slight, if strained, smile from Elizabeth.

She sighed. “We’ve just had our weekly status dial in with the SGC. We informed them in last week’s data burst about the treatment’s lack of effect and received their reply today.”

They want us removed from command,” John stated with grim certainty.

What? No, we can still do our jobs,” Rodney argued. “We’re still us, despite appearances to the contrary.”

There are concerns that you won’t be able to handle your duties effectively.” She held up a hand to forestall any protests. “I can see where they are coming from as I have heard from several staff members who have expressed discomfort. It doesn’t mean that I agree and I am doing my best to fight it.”

But?” John prompted, knowing there had to be more.

They are still debriefing Colonel Caldwell and the Daedalus hasn’t reached Earth yet. But I’ve been informed that once it does, it will be immediately dispatched back here with a delegation from the IOA to hold an inquiry into recent events. The results of said inquiry will decide who remains in command here.”

It’s not just us on the line, is it?” John asked with sudden awareness. “They’re threatening you too.”

She nodded. “And Carson. They’re not happy with any of us with regards to recent events.”

That’s absurd! It’s not like we could have foreseen this happening!” Rodney was working himself into a temper.

No, but can you honestly tell me that every precaution was taken? That things were handled according to protocol?”

Rodney deflated. “You know I can’t. That retrovirus shouldn’t have left Atlantis.”

And that is part of the reason for the inquiry.”

So what can we do?” John asked.

I have read all of the medical reports. They all agree that despite your physical appearances you are mentally yourselves. So I am ordering an end to your confinement to quarters.”

Finally!” Rodney burst out.

She held up a hand. “I’m not finished. You need to be seen out and about. Interact with people. It will be uncomfortable but you need to let them get used to seeing you like this to see if they can still work with you if there is to be any chance of you remaining here.” She couldn’t meet their eyes.

Wait, wait, wait. What do you mean if? Where else could we go?”

It’s possible the IOA will order you to return to Earth.”

John’s blood ran cold at the thought. Not only leaving Atlantis but what their lives would be like if that came to pass. “Elizabeth, look at us. There’s no way we could live any sort of life on Earth.”

Rodney was nodding along frantically. “We couldn’t go out in public. They’ll throw us into a deep hole and forget about us.”

I will do everything in my power to see that that doesn’t happen,” Elizabeth promised. “Hence, the need to get people here used to you and on your side. However, we need to make sure everything is above board to keep the IOA from finding fault with our actions. So while you are no longer restricted to quarters, your access to high-security areas is still restricted. That means the Stargate, Jumper Bay and Armory.” She took a deep breath and turned to face Rodney. “I am not completely restricting your access from the labs. However, I am requiring that you be supervised and that Dr. Zelenka checks over your work.”

What?! Elizabeth-”

I’m sorry Rodney but otherwise the IOA will use it as an excuse to remove all of us.” She gave him an apologetic look.

Yes, fine, whatever,” Rodney gave in gracelessly.

John understood how he felt. Being denied access to the jumpers felt similar for him. “Anything else?”

Elizabeth seemed to brace herself. “I need you both to meet with Dr. Heightmeyer.”

John sat up straight and glared at her. “We’re fine, Carson said we’re ourselves again.” Beside him, Rodney was unexpectedly silent.

I know what Carson said but you’ve both been through what could be considered a trauma. You are definitely going through some unexpected and unwanted changes. I think it would be best if you talked things over with a professional rather than letting things fester.”

John opened his mouth to disagree.

Elizabeth gave him a sharp look. “It’s no different from you asking Kate to speak with Teyla about her nightmares before the Siege,” she pointed out.

John deflated slightly, then gave her a sharp nod. “Fine,” he gritted out as he worked to push his anger down. “Anything else?” he asked again, his tone back to normal.

She shook her head. “Just try to follow protocol.”

He smirked at her. “Hey, it’s me.”

She gave him a wry grin. “I know, that’s what I’m worried about.”

With that, he and Rodney stood and exited the office, heading toward the transporter. Their Marine escort followed them until they had exited the Gate-room, as their access to that area was now considered restricted. But once they exited, they were finally free from supervision for the first time in weeks. “So, Mess?” John asked.

Rodney hesitated, then shrugged. “I could eat.”

John snorted. “You can always eat, McKay,” he said as he selected the destination closest to the Mess.

Hey, what is that supposed to mean? I have a medical condition, I need to eat regularly, otherwise I become hypoglycemic. You wouldn’t want me to end up-” he trailed off as they entered the cafeteria and the noise level instantly plummeted.

The two of them stopped dead just inside the entryway as they noticed the attention they had drawn. Some people were outright staring, others were trying to be subtle about it and looking from the corners of their eyes. And some people were determinedly not looking in their direction at all.

John swallowed. For a few moments, bantering with Rodney, it had been so easy to forget that they weren’t the same any more. Keeping his face carefully blank, he nudged Rodney toward the food line. He saw Rodney’s face, expressive as always, fall as several people immediately left the line, hurried excuses falling from their lips as they headed for the door.

John calmly picked up a tray, nudging Rodney to do the same and moved up to the server. “So, what’s good today?” he asked as nonchalantly as possible.

The server, Corporal Evans if he recalled correctly, was unable to meet his eyes. “Um, there’s, uh,” she stammered.

He felt his patience wearing thin. “You know what, just give me some of that, that and that,” he pointed to various dishes without really paying attention, his appetite gone. Still, Elizabeth had said it was necessary to get them used to them and he could see the point. “Thank you,” he said politely, if a bit stiffly, once she had served him and Rodney, who had indicated for her to give him the same as John.

Sir,” she mumbled, her eyes still on the food.

Meal collected, John headed for a table near the far wall that didn’t have any other occupants nearby. While he would do his best to comply with Elizabeth’s orders, he could only put up with so much at a time. He sighed as he sat down, his back to the wall. “You okay?” he asked Rodney who merely shrugged. Concern filled him at the unusual silence from the genius. “So, do anything interesting this past week?” he asked, hoping to draw him out.

Rodney sighed as he poked at his food with his fork, not eating it. “It’s not like I was expecting a warm reception. I just-” he broke off, waving a hand around absently.

I know buddy, me too.”

They sat there a few moments, contemplating their trays as the noise level slowly began to return to normal levels. But it was obvious what the main topic of conversation was; would have been obvious even without John’s newly enhanced hearing. He found himself glaring at one man in science blue who had been complaining about having to eat in the same room as the ‘freaks’. The man must have felt his gaze because he turned his head and looked at them before paling and beating a hasty retreat.

Rodney snorted beside him. “What a useless idiot, almost as bad as Kavanagh. What the hell the SGC was thinking when they sent him out here, I haven’t a clue. He won’t last long.”

Glad to have McKay finally speaking again, John was about to ask about any other new scientists when a tray was plopped down on their table, Ronon practically throwing himself into a seat.

Hey, you’re out,” he said with a grunt.

Obviously,” Rodney said, rolling his eyes. “Hey, you’ve got your own,” he protested when Ronon made to snatch a piece of fruit off of his tray. All three of them blinked in surprise when he successfully blocked Ronon’s move.

Huh,” Ronon said thoughtfully, before trying again. “Your reflexes are better,” he said when he was again blocked. “Should get you to the gym, see what you can do.”

No way in hell!” Rodney immediately began protesting that idea.

But John could see the point. “We really should find out what our bodies are capable of.”

Am I interrupting?” Teyla asked as she stopped before the table, a tray held in her hands.

Teyla,” John greeted, a smile beginning to form for the first time since they entered the Mess. “Of course not. Join us?” His smile faded as she didn’t quite meet his eyes.

I am afraid I can not. I just wanted to say how glad I am to see you and Dr. McKay have rejoined us.” But there was something off in her tone.

John winced as he recalled the disastrous ending to their last sparring session. “Look Teyla, you got a minute?” He ignored Rodney’s curious look. “Please?” he asked.

Alright,” she acquiesced reluctantly.

Be right back,” John said to the other two men, then led her to a nearby corner. Thankfully Ronon took the opportunity to try to snatch something else from Rodney’s tray, distracting him from listening in. This was one conversation he didn’t want to be overheard. “Look, I owe you an apology. I’ve been remembering things, some things I might have done that you could call out of character.”

Like attacking your security detail?” she asked.

That was one of them. But not what I wanted to apologize to you for.”

She shook her head. “You were not yourself. Give it no further thought.” But he noticed as her hands tightened on her tray.

I don’t want to make you uncomfortable-”

Then please forget about it.” She sighed. “It is not your fault. I must simply work through some things on my own.”

John stared at her for a moment. “Alright, if you’re sure.”

I am.” Teyla turned to walk away, then paused and glanced back at him. “It really is good to have you back. John.” With that, she turned and walked away.

John shook his head and headed back to the table. His eyes widened in shock at the scene before him.


Rodney stared suspiciously after John as he led Teyla away for a private conversation. He was considering using his enhanced hearing to listen in when Ronon made another play for his food, distracting him. “Would you stop that already? You have a tray of your own, why must you insist on stealing my food?”

Ronon shrugged. “You’re not eating it, don’t want it to go to waste.”

Rodney glared at him, then picked up his fork and took a bite, chewing it exaggeratedly. “There, happy.” He blinked. “Huh, that’s really good. What is that?” He quickly took another bite, his eyes closing in bliss. He’d never tasted anything so good before.

Hey Rodney, you’re looking a bit blue.”

He groaned at the annoyingly familiar voice, opening his eyes to see Lieutenant Cadman, smirking down at him. “Go away. I’m not in the mood to deal with you today.”

Come on Rodney, we’ve missed your delightful presence these last few weeks.”

Go away,” he repeated, taking another bite of the delicious food on his tray.

Come on, is that any way to-” Cadman started to say before stopping and staring at the food on his plate. Her eyes went wide and she immediately made a grab for the dish.

But Rodney’s improved reflexes allowed him to snatch it up before she could. “What is with you people. First Ronon, now you. Get your own!” He snapped, taking another big bite.

Rodney don’t!” Cadman said as she again lunged for his food. “That’s got lemon in it!”

What?!” Rodney asked in shock, pausing mid-dodge and thus ended up tackled and pinned by Cadman as she tried to wrestle the delicious food away from him. He took a moment to check his body’s reactions. No, he didn’t feel like he was swelling up or having any difficulty breathing. Cadman was wrong.

What the hell is going on here?” John asked, bewildered, as he returned to the table, which was once more the center of attention.

Cadman finally managed to pry the dish from Rodney’s hands and she hastily stood up. “Sir! We have to get Rodney to the infirmary. I don’t know how much he’s ingested.”

You’ve got to be wrong Cadman, I feel fine. Now give me my food back and go away,” Rodney demanded.

Cadman?” John questioned.

Sir, he was eating the pasta, which I know has lemon in it. It was clearly marked.” She turned to Rodney. “How did you not see the sign?”

I wasn’t paying attention,” he admitted. “But you’ve got to be wrong. I feel fine.”

Come on buddy, we’re gonna pay Carson a visit, just to be on the safe side,” John said, giving Cadman a nod of thanks.

But I feel fine!” Rodney protested.

Humor me.”

Oh fine,” Rodney grumbled.

Does that mean you aren’t going to finish that?” Ronon asked, already helping himself to the remains of Rodney’s meal.

John grabbed Rodney by his arm and started pulling him toward the exit before he could reply.

A short time later found them in the infirmary, with Carson shaking his head. “Well, as near as I can tell you’re perfectly healthy. Though with your changed DNA and physiology it’s no wonder your allergies have changed.”

Rodney’s eyes widened in wonder as he thought about that. “You mean citrus won’t kill me anymore. I can actually eat lemon meringue pie, lemon chicken, orange chicken...” he trailed off as he contemplated the foods he’d never been able to eat before.

Aye, it seems that way. Though we’re going to have to run some tests and see if there are any other changes. You might be allergic to something you weren’t before,” Carson pointed out.

Rodney groaned at the thought of more medical tests. “You and your voodoo. Didn’t you do enough testing before you released us?”

John patted him on the shoulder. “Don’t worry, I’m sure it won’t take long. And it’s for your own good.”

Glad you feel that way Colonel,” Carson said as he waved over a nurse. “Since we’ll need to run the same tests on you.”

It was John’s turn to groan while Rodney gave him a smug look.


It was several hours later that they were finally released, minus some blood. “Leeches,” Rodney grumbled. He glared at John. “This is your fault for making me come here. I said I felt fine.”

Well, at least now we know you’re no longer allergic to citrus.”

There is that,” Rodney agreed. “So now what?” Since their little foray into the Mess didn’t seem to be much success.

I know you probably want to get to the lab and see what’s been going on but it’s kind of late to try to catch up on what you’ve missed. So why don’t you start fresh tomorrow?” John suggested.

Rodney eyed him suspiciously. “Depends, what are you planning?”

Well, Ronon did have a good point. We really should see just what our bodies are capable of now.” He held up a hand to ward off Rodney’s protest. “Come on, it isn’t that much different than Carson running tests to see what’s changed for us. This is us figuring out our limits. Haven’t you noticed your reflexes are faster? You could be stronger, faster. We really need to know what we’re capable of before we go out in the field again.”

Right, like we’re ever going to be able to go out in the field again,” Rodney pointed out. “Alright fine,” he hastily agreed when John’s face fell at that reminder. “But you owe me.”

John grinned at him. “I’ll make it worth your while,” he promised as he hurried Rodney along to the gym he usually used.

They paused in the doorway upon spotting the room already occupied. They watched for a few moments as Teyla and Ronon used the bantos rods before Teyla got the upper hand and managed to disarm Ronon.

They stopped and took a step back, then glanced at the door. “John, Rodney,” Teyla acknowledged politely, if a bit coolly.

Sheppard, McKay,” Ronon nodded.

Sorry to disturb you; didn’t know anyone would be here,” John apologized.

It is no bother,” Teyla said, moving to put her bantos rods away. “So you were not looking for us?”

Nah, figured we’d do like Ronon suggested and see what our bodies can handle.”

That so?” Ronon asked, as he picked up one of the rods and twirled it. “Happy to help,” he added with a wicked grin.

Er, you know what, I think I’ve changed my mind,” Rodney said as he started to back away only for John to grab his arm.

I would also be willing to assist,” Teyla offered.

There, see? Teyla won’t do anything you can’t handle,” John pointed out.

Fine,” Rodney gave in.

Which how he found himself getting knocked to the ground and pummeled with a stick a short time later. “Ow,” he complained before realizing that it didn’t actually hurt. He rose to his feet. “Hey, hit me again. Oh, but not too hard,” he told Teyla.

She looked at him, eyebrow arched, then did as he asked.

Rodney grinned at her. “It doesn’t hurt. Try again, a bit harder.”

She whacked him in the chest.

Still doesn’t hurt,” Rodney boasted, grinning widely as he rocked back and forth.

Huh,” Ronon said as he came over and poked at him. “Scales must act like armor. See how they’re thicker where you’d be most vulnerable, your neck, your chest.” He smacked a hand against each body part he named, circling around Rodney. “But doesn’t mean you can’t be hurt,” he added as he grabbed him and threw him to the ground, following him down with a knee to the back.

Ow,” Rodney moaned.

That’s why you gotta practice,” Ronon said as he regained his feet then reached down to haul Rodney up.

Maybe I should watch for a bit. Why don’t you beat up on Sheppard for a while,” Rodney suggested hopefully only to get a dirty look from John.

Come on, I’m gonna try to hit you and you’re going to dodge as fast as you can,” Ronon told him instead.

Oh joy,” Rodney mumbled, hating his life.


That wasn’t so bad,” John said as he walked with Rodney back to his quarters, only to receive a glare from the scientist.

I hate you so much right now.”

No, you don’t.”

Oh yes, I do. Now I’m all sore, probably covered in bruises,” Rodney complained as he waved his hand before his door to open it.

John followed him in. “Want me to kiss them and make them better?”

Rodney froze, gaping at him.

John waggled his eyebrows suggestively.

Rodney snorted and rolled his eyes, paralysis broken. “For a minute there I thought you were serious,” he said, sounding disappointed.

John frowned. “I was serious.” He reached out, laying a hand on Rodney’s shoulder. “You haven’t changed your mind, have you?”

I haven’t but I thought you might have,” Rodney admitted. “I mean, you had plenty of time to think about all the things you stand to lose. Your career-”

John cut him off. “I doubt very much I have a career left at this point.” He gestured to himself to emphasize his point. “But even if I did I wouldn’t care.”

Rodney gave him a skeptical look.

Okay, I probably would care. But I would still want this, want you.” He reached out to rest a hand on Rodney’s cheek. “Okay?” he asked as he leaned in.

Rodney nodded, eyes wide as he leaned toward John.

Their lips met. It started out slow, a simple firm press of lips. Then it became hot and wet, hands roaming each other’s bodies, clothing being removed.

A while later found them lying tangled up together in Rodney’s bed, satiated. John breathed in deeply, enjoying their mingled scent that filled the air, the feel of the warm body he was wrapped around. “I should go,” he said reluctantly, not wanting to move.

Or you could stay,” Rodney mumbled sleepily.

John smiled. “I can stay,” he agreed, curling his body a bit more around Rodney. Contentment filled him like never before and he drifted off with the sound of Rodney’s soft snoring filling his ears.

Chapter Text

John strode through the corridors, nodding acknowledgment to those he passed as he made his way to the main lab. It was getting close to dinner time and thus it was time to retrieve Rodney. He had plans. A small smile formed as he thought about the last week or so.

John and Rodney had settled into a routine. They would eat together in the Mess, usually joined by Ronon and Teyla, and sometimes others like Carson, Cadman and Zelenka. Then they would split up, Rodney heading to the lab with Zelenka while John either worked out in the gym or found something else to keep himself occupied. He’d even taken the time to complete some of his paperwork, a sign of just how bored he’d been.

John had even gone over the changes Caldwell had tried to implement. Some of them were obviously designed to give him, and thus the Goa’uld controlling him, more control over the city. But a few did seem to have merit. Things John had overlooked with his previous lack of command experience. He would have to talk with Elizabeth about seeing them implemented. One of the ideas that had caught his interest was having any teams in a hostile situation dial a beta site instead of coming straight back to Atlantis in order to keep their gate address secure. It was definitely something they should have considered before.

Occasionally, John would wander down to the lab to see if anything interesting was happening and to perform light switch duty. He had grudgingly cleared that with Elizabeth and it was decided that, like Rodney, as long as Zelenka was present as nominal supervision then it was fine.

Thankfully the changes he had gone through hadn’t negatively affected his or Rodney’s ATA genes. If anything he thought Rodney’s had gotten stronger though he hadn’t said anything about his suspicions yet. His own connection to Atlantis was just as strong as ever. He gave the wall a pat as he thought that, enjoying the gentle hum in the back of his mind as he continued to reflect over recent events.

John was happy to see that for the most part, the scientists reacted normally to both Rodney and himself. Sure, there had been some hesitation the first day but, after Rodney tore into a couple of them for messy math or careless mistakes, things had gone back to normal. It was only a small handful, all newcomers, who seemed to have a problem with them. John was keeping an eye on them but other than a few pointed comments nothing had been said or done.

He was also seeing an improvement on the military side of Atlantis. They were no longer the center of attention when they entered the Mess. Everyone was slowly getting used to the sight of their changed appearances. John thought his sparring sessions with several of the Marines might be helping that. It seemed that his new ability to put them down on the mats was winning them over. Like the scientists, there were a few holdouts, but John could tell that Elizabeth’s plan was working.

Even the appointments with Dr. Heightmeyer hadn’t been too bad. She hadn’t tried to make him talk about his past which he found was a plus. She asked him questions about his interactions on Atlantis, if he was finding it difficult to assimilate to his new circumstances. But at the same time, she didn’t dig too deeply if he had difficulty answering a question, something he appreciated. At the last session, she even admitted that she thought he had a good handle on things and had said they cut their sessions back to weekly instead of every other day.

The only sore point was that his relationship with Teyla was still strained. Their interactions remained civil but cool. John was beginning to suspect that her aversion had less to do with his actions and more to do with his new appearance as he had noticed that she was reacting similarly to Rodney. He could only hope that it was a simple matter of getting used to their appearances.

John also made sure to get Rodney out of the lab and into the gym for an hour each day to work off some of the excess energy that they both seemed to have. Rodney complained each time but he always went and was showing an improvement in his hand to hand skills.

Of course, John always made it up to him at night. His favorite part of their new routine was that after dinner they would head to one of their quarters, usually Rodney’s as he had the bigger bed, and spend the night together.

He reached the lab door and his smile widened. Time for dinner, then ‘dessert’. “Alright McKay, feeding time,” he called out as he entered the lab.

Rodney shot him a look, then went back to typing on his laptop. “Busy.”

But Zelenka looked up and gave him a grateful look. “Yes, please, take him away. Could use a break.”

Rodney glared at him. “I don’t need a break.”

I do,” Zelenka shot back.

John interrupted when Rodney started to gear up for a rant. “Okay, come on Rodney. You’ll feel better after you eat something. Plus we have plans later.”

We do?” Rodney asked. John gave him a look. “Oh, right, yes. See you later Zelenka, don’t blow anything up while I’m gone,” he added as he saved his work and powered down his computer, grabbing his tablet on the way to the door.

They ignored the complaints muttered in Czech as they left. John let Rodney ramble on about his work and complain about the impracticality of having Radek supervise his work as they entered and then exited the transporter. They were just coming into sight of the doors to the Mess when there was a pulse of energy that spread throughout the structure and an alarm began to blare.

What the hell was that?” John asked, hurrying over to a nearby scientist who had collapsed when the energy wave hit. He checked his pulse. “He’s stunned,” he said, then glanced through the open door to the Mess, spotting all of the unconscious people lying there like puppets whose strings had been cut. “They’re all stunned.”

Rodney was frantically tapping away at the tablet. “Oh no! This is not good, not good at all.” He turned it to show John footage from the Gate room. “Wraith,” he said needlessly, the image showing a handful of Wraith moving through the Gate room among unconscious personnel. A large, bluish glowing orb sat in front of the gate.

Shit. Can you lock them down in there?” John asked, mind working to come up with a tactical plan. “Is anyone else still moving?”

Not in this tower. I don’t know about further away. Okay, they’re sealed into the Gate room for now. But that doesn’t buy us a lot of time.” Rodney was frowning worriedly as he stared at the tablet. “At least it doesn’t look like they’ve fed on anyone,” he said. “Yet. They seem to be focused on trying to access the equipment. Probably to send a signal to all of their buddies that we’re still here,” he finished morosely.

I know. First stop is the armory, you’re going to have to override our lockout. Then it’s up to us to take them out.”

Rodney shot him a look. “Just the two of us?! Are you nuts?!”

We’re the only ones still moving,” John pointed out. “And we have to hurry before they manage to signal a hive or dial out to tell other Wraith that Atlantis is still here.” With that said, John herded Rodney back to the transporter and selected the location nearest the armory.

It took Rodney only a minute to override the lock. John glared at it. “Do we need to update our security protocols?”

Please, as if anyone else could get through them. At least not that quickly and not without setting off alarms,” he added after a moment’s thought.

John let it go, there were more important things to worry about. He grabbed a handgun in a thigh holster and gave it a quick look over before strapping it on, dimly aware of Rodney copying his actions. He started to reach for a tactical vest and paused, considering it before skipping it.

No vest?” Rodney questioned.

John shook his head. “Been having too much trouble finding clothes that fit right, with the scales and spikes. We don’t have time to waste figuring out how to make a vest sit right.” And it was dangerous to go into the field in an ill-fitting vest. If it slipped at the wrong moment it could impede movement at a critical moment.

Right, okay,” Rodney agreed nervously.

It’s gonna be alright,” John told him, taking a second to give his shoulder a brief squeeze. “We’ve been through worse situations than this and come out on top. We can handle this.”


John grabbed a couple of P-90’s and checked them over quickly, then handed one to Rodney along with extra clips. He stuffed his own clips into his pockets, then grabbed a few more things that might come in handy before ushering Rodney out the door and toward the transporter.

They stepped into the transporter and John paused, considering which option would be better. The transporter in the corridor outside the Gate room or the one in the control room. “Pull up the security footage, can you see where all the Wraith are?”

Rodney did so and they both studied the images. There was one drone and a soldier up in the control room, while two other drones were pacing around the gate room floor. The last Wraith, another soldier was in Elizabeth’s office, poking at her computer. John’s blood ran cold at the sight of it so close to her unconscious and defenseless body. “Can you tell what he’s doing?”

Rodney took back the tablet and typed rapidly. “Looks like he’s trying to gain access to the computer network but is having trouble with the firewalls. The lack of knowledge of our written language is probably also throwing him off. But he is making significant progress despite those limitations. There, I threw up everything I could quickly to block him but I don’t know how long before he’ll get through.”

John nodded as he came to a decision. “We’ll enter through the control room. I don’t want to leave Elizabeth vulnerable to that thing longer than necessary. So we select the Control room as our destination, weapons ready. As soon as the doors open we take out the two in there. Then I’m going to go after the one in Elizabeth’s office while you provide cover fire on the two downstairs. You should be able to easily hold them off until I can get back and help you take them out.”

Rodney stared at him. “John-”

You can do this,” John told him, giving his shoulder another squeeze. “I’ve got faith in you.”

Alright but you better not get yourself killed,” Rodney warned as he reached up and squeezed the hand on his shoulder.

John nodded, then readied his P-90 and stepped up to the control panel. “Ready?” he asked, hand hovering in front of it.

No,” Rodney admitted, taking a deep breath and lifting his own weapon, stepping to one side of the transporter doors so he’d have some cover. “But do it anyway.”

John pressed the Control room location and entered his access code, then stepped to the other side of the door. From this angle, he should be able to see into the room while still having some cover.

The doors slid open, the sound drawing the attention of the Wraith. John watched as they turned to face the transporter, then he swung partway out into the opening and with a quick glance to check their line of fire he began firing at the soldier. Beside him, Rodney mirrored his actions with the drone.

Despite the first few shots hitting them in the center of their chests, the Wraith staggered but didn’t fall. Instead, they reached for their weapons and began to return fire.

John flinched as he caught part of a stun blast but when there was no noticeable effect he ignored the incoming blasts and kept firing. Seconds later their efforts paid off as first the drone and then the soldier collapsed. John stepped out of the transporter completely and fired a couple of bullets directly into their skulls to ensure they wouldn’t be getting up again. He glanced quickly over the balcony, then fired a few rounds to keep the Wraith there occupied until Rodney joined him.

Go,” Rodney said as he took over firing down at the Wraith drones. “And be careful.”

John checked then replaced his clip before hurrying to Elizabeth’s office. A stun blast hit him before he even reached the doorway but again had no effect so he kept moving forward, ignoring the subsequent stun blasts.

The Wraith scowled at him then reached down and pulled Elizabeth up. “Fire and I’ll use her life force to heal the damage,” he threatened.

John scowled, keeping his weapon trained on the Wraith. “Let her go.”

The Wraith laughed. “I believe we are at an impasse unless you care so little for her life.” He moved his hand toward Elizabeth’s chest.

John saw red as rage filled him. He was not going to do this again, watch as a Wraith fed, leaving him only the option of providing a mercifully fast death. Without thinking he dropped his weapon and launched himself at the Wraith, his unexpected speed allowing him to knock the Wraith away from Elizabeth.

They rolled on the ground, wrestling for the upper hand. John felt his shirt rip during the struggle. “Fool,” the Wraith sneered as it managed to momentarily get the upper hand, rolling on top of John and plunging his hand toward John’s chest.

John flinched at the sensation of the feeding slit against his bare chest and waited for the expected pain. After a few seconds of nothing happening, he opened his eyes to see the Wraith staring down at him in shocked horror, having finally noted John’s odd appearance.

What are you?”

A dark grin, more of a baring of teeth, crossed John’s face. “Your death,” he replied as he freed an arm and threw a punch at the Wraith, knocking him off of him. He followed up with a few more strikes then grabbed the Wraith by the neck and with one quick movement snapped his neck. He dropped the body to the floor then pulled his sidearm and fired two bullets into the skull. “Heal from that,” he spat before turning to check on Elizabeth.

Elizabeth was still stunned and she appeared unharmed. She definitely hadn’t been fed on he found to his relief. So he did his best to put her in a more comfortable position. “Sorry about the mess,” he told her in case she was able to hear him.

Suddenly he became aware that it was too quiet, the sound of gunshots from the Control room had ceased. “Sheppard!” Rodney’s voice was panicked before being cut off.

Fuck!” he cursed, momentarily having forgotten about the firefight still going on outside. He snatched up his P-90 and raced back outside.

His eyes widened as he spotted one of the Wraith drones holding Rodney by his neck while its hand with the feed slit was held against Rodney’s chest. Fear filled John at the sight, for while the Wraith hadn’t been able to feed off of him that didn’t necessarily mean the same for Rodney. He snapped his P-90 up but couldn’t get a clear shot without risking hitting Rodney.

As he was about to drop his weapon and tackle the Wraith, Rodney managed to twist his arm and elbow the drone in its chest. It immediately let out a shriek of pain and dropped him, before falling down itself.

John wasted no more time and fired several times into the drone, including a few head shots to be certain it was dead. Spotting movement from the stairs, he turned and took out the last drone before dropping to his knees beside a panting Rodney.

It’s about time!” Rodney panted out when John reached out to check him over.

Sorry.” Guilt filled him as he wondered if he had taken too long in dealing with the Wraith. Should he have done things differently? But that would have put Elizabeth at risk. He started to second guess his actions.

Oh stop it,” Rodney said as he got a look at his face. “I didn’t mean it, I know you were busy yourself. Is Elizabeth ok?”

She’s fine,” John reassured him before turning and frowning at the scene before him. Something wasn’t adding up. “How did that drone get the drop on you?”

A somewhat sheepish, yet defiant look crossed Rodney’s face. “They weren’t as stupid as drones usually are. They realized I couldn’t cover both of them at the same time if they split up.”

John glanced from the Wraith that had been attacking Rodney to the one that had only just made it up the stairs. “Okay, so why didn’t you focus on the one that was closest? Do we need to have remedial lessons on situational awareness and dealing with the more pressing threat?” Had Rodney been careless with his own safety?

Rodney glared at him. “Well excuse me for not wanting to watch them feed on our people! After they figured out I could only pin one of them at a time they also realized that I was being careful about not hitting any of the unconscious men down there. They then gave me the option of either keeping them both down there while they took turns feeding, or letting one get close while I kept the other away from our defenseless personnel. Forgive me for expecting you to get back here faster to help!”

Renewed guilt filled John. “Sorry,” he apologized again. He hadn’t meant to take so long. And of course, Rodney didn’t want to let the Wraith feed on the defenseless men.

Rodney sighed. “I didn’t mean it that way. It’s not your fault.”

John didn’t quite agree but decided to change the subject. “What is that thing anyway?” he asked as he pointed to the glowing orb in front of the Gate.

Rodney shot him a look, silently telling him that he knew what John was doing and he’d go along for now but they would be talking later. John hoped he’d be able to provide further distractions when the time came.

Instead, Rodney grabbed a tablet from in front of one of the stunned technicians and they moved down the stairs and stopped right in front of the orb. “What is it?” John asked again after Rodney had walked around and examined it.

Huh,” Rodney said, again looking at the orb then at the men on the floor directly in front of it. “It looks like Sergeant Stackhouse’s team was returning from a mission when this happened.” He turned to his borrowed tablet and pulled up the footage from earlier. “There.”

John moved closer to watch as one of the men came through the Gate gesturing for the guards to be prepared. Stackhouse and another of his team came next, supporting a third stunned man. Before the shield could be raised over the Gate the orb came through and released the pulse of energy that he and Rodney had felt earlier, causing everyone in the room to collapse. Then the five Wraith stepped through before the Gate shut down.

Damn,” John said, wishing he had spoken to Elizabeth earlier about a beta site. This was too close. He kept watching as the Wraith in the footage examined their surroundings. The apparent leader of the group, the one that had been in Elizabeth’s office, seemed surprised and possibly angry about their surroundings. So they hadn’t expected to end up in Atlantis?

When the footage they had seen earlier began to play he motioned for Rodney to stop it. Then he turned and glanced at the orb, frowning. “Is it keeping everyone stunned? Will it send another pulse out?” He unconsciously reached for his P-90, wondering if they should just destroy it.

I don’t know yet,” Rodney said distractedly as he studied the orb. “Hmm.”

Before John could find out what Rodney was thinking the doors to the Gate room burst open and a handful of men came storming in. “Freeze!”

Easy guys, it’s been taken care of,” John said, as he slowly turned to face them, purposefully keeping his hands clear of his weapons.

Colonel Sheppard? You’re not supposed to be in here,” Captain Martelli said. “What’s going on?”

Captain, where did you come from? Before you came in, I mean,” Rodney interrupted, snapping his fingers.

Martelli frowned. “We were out doing a patrol. We were on the West Pier when we lost communications and when we got back to the Central Tower everyone was unconscious. What happened?”

The effects, while wide-spread obviously have a limited range. Didn’t reach the West Pier but everyone in this tower was affected. Huh,” Rodney muttered as he began to tap away again at his borrowed tablet, ignoring everyone else.

John shook his head at him then addressed Martelli. “We had a visit from some Wraith,” John told him, gesturing up the stairs to where one of the drones could just be seen. “Seems they have a new toy that can stun everyone in a wide area.” He gestured to the orb. “Neither of us were affected but when we saw there were Wraith in the city I decided we didn’t have time to waste in getting here and stopping them. We didn’t know how far the stunning effect had reached or if there was anyone else who hadn’t been stunned.”

And the Wraith, sir?”

Dead.” John gestured up at the Control room.

At that, the soldiers finally relaxed their stances. “Orders sir?” Martelli asked.

John shrugged. “I’m still out on medical so I technically can’t give you orders. But I might suggest making people comfortable while we see how long it takes the stunner’s effects to wear off.” He paused and looked at Rodney who was now poking at the orb. “Unless that thing’s going to go off again?”

Rodney ignored him. “Let’s see, if I- Yes!” He exclaimed as the orb went dark. He turned to John with a smug grin on his face. “I’ll want that delivered to the lab for study. Just imagine if we can replicate the effect.”

John could easily imagine it. “Okay. But it’s off now, so our people should start recovering soon?”

Rodney shrugged. “Like I said, I have to study it further. But my best guess is that it just amplifies a normal stun blast to have a wide affected area. Everyone should start recovering just like they would from a regular Wraith stunner.”

Relief flooded through John at that news. “Okay, so I guess we just wait then. Let’s start making people comfortable.” He arched an eyebrow at Rodney when he opened his mouth to protest. “Unless you would want to be left where you fell if this happened to you?” Rodney shut his mouth. “Didn’t think so. Let’s go.”


Rodney looked up from his tablet, absently munching on a power bar, when Elizabeth cleared her throat. She raised an eyebrow at him when he finally met her gaze. With a huff of irritation, he closed down the files he was working on and put the tablet to the side. How was he expected to get any work done analyzing the orb when first he’d been put to work moving unconscious people and then Elizabeth had called for a debriefing as soon as people began to recover.

Thank you,” she said to him before turning to face everyone else gathered at the conference table. “Now, let’s get started, shall we? What do we know and how can we prevent this from happening again in the future?”

Rodney glanced around at the rest of the occupants. He and John were there of course, as was Major Lorne who was technically in charge of the military personnel while John was ‘on medical leave’ as well as Radek who was similarly supposedly in charge of the science division. Also present was Sergeant Stackhouse and his team as well as Captain Martelli. Teyla and Carson rounded out the rest of the group.

Ma’am,” Stackhouse began. “We were exploring PX5-083 having heard that there might be some Ancient ruins there. We hadn’t gone too far from the Gate when we were attacked. Jenkins was hit by a stun blast. We returned fire, then retreated back to the Gate and dialed Atlantis.”

Elizabeth frowned. “Were the Wraith specifically there for you? Was it an ambush?”

Stackhouse looked uncomfortable. “I don’t know for sure but it seems that way. They were too prepared to have just come across us by chance. And that orb that knocked everyone out doesn’t seem like the type of thing they would have on them by chance.”

Elizabeth glanced around the table, a worried frown creasing her forehead. “Is the city at risk? Do they know that we tricked them into thinking we destroyed it?”

I don’t think so,” John said, shaking his head. He was slouched in his chair as usual. “From the footage Rodney was able to pull up, the Wraith were surprised to find themselves here.” He hesitated. “My best guess is that they figured that some of us evacuated before we ‘destroyed’ Atlantis. They are probably trying to find survivors in order to find Earth’s location.” A frown crossed his face. “Where did the information about the ruins come from? If the Wraith still believe we destroyed the city they probably think we’re looking for whatever technology we can scavenge, so it would make sense for them to stake out known outposts. But they had no way of knowing our men would be at that specific site unless they had inside information.”

We learned about the ruins from a contact on Manaria,” Elizabeth admitted.

Rodney saw John’s eyes widen in shock before a look of anger crossed his face as he straightened up from his slouch. “Manaria?! You sent a team out based on information from those bastards? You know I haven’t trusted them since they sold us out to the Genii.”

Rodney could understand John’s anger, feeling a twinge in the scar on his arm as he remembered those events. A glance at Teyla showed she was uncomfortable at the mention of the Manarians’ previous betrayal that had cost the life of an Athosian.

Elizabeth’s expression was blank. “The Manarians apologized for that. And they have been a valued trading partner since then.”

Until they decide to stab us in the back again. Case in point.”

We have no proof that Manarians were aware this was a trap,” Elizabeth pointed out.

Are you kidding me?!”

She held up a hand. “However, I agree that we will be more careful about following up on any information we receive from them. We can discuss that issue in more detail later. For now, let’s get back to the main reason we’re here.”

The briefing continued. Every action was gone over. They even brought up the footage from the Gate room and the Control room. Rodney didn’t know what to make of the looks he received when the footage of him defending the defenseless personnel was played. However, those looks were quickly forgotten as he saw the footage from Elizabeth’s office. “You were fed on?!” He looked at John in shock.

It tried but nothing happened,” John quickly tried to reassure him. “I don’t think it could get through the scales.” He looked a bit self-conscious at the reminder.

Everyone was looking interested at this information. “Did you have any idea that it wouldn’t be able to feed?” Lorne asked.

No, I was as surprised as he was when it didn’t work.”

Rodney suppressed a groan when he saw the excited gleam in Carson’s eye. Great, more tests in their future.

There were more questions once they got to the footage of the drone getting the drop on Rodney only for him to manage to free himself. “Wait, what was that?” Lorne asked. “What did you do?”

Rodney frowned. “I elbowed it, I was just trying to get it to loosen its grip.”

Yeah, but what caused that reaction? Even if your strength has increased a simple blow from an elbow shouldn’t have caused that type of reaction.”

Carson’s eyes widened and the excited gleam increased. “Of course! Those spindly protrusions you have must act like a stinger. I wonder if you’re capable of producing and injecting venom?”

Rodney’s frown deepened as he self-consciously touched one of the spiked protrusions. “But they’re not sharp or even that hard.”

They probably hardened in response to the adrenaline in your system. We’ll have to run more tests to be sure but we are learning new things about your changed physiology all the time. This is all new ground to cover.”

This time Rodney allowed the groan to escape.

Elizabeth quickly got the meeting back on track again. “As fascinating as all of this is, what I want to know is what we can do to prevent something like this from happening again.”

Well, not trusting the Manarians would be a good starting point,” John shot out.

Colonel,” Elizabeth said, her tone full of warning.

He sighed. “I did actually have a suggestion. It’s one of the changes that Colonel Caldwell tried to implement before we learned he was being controlled by a Goa’uld and halted all of them. He suggested creating a beta site for all teams in hostile situations to travel to first instead of coming straight back to Atlantis. The idea has merit and I had planned to bring it up with you as soon as possible.”

Wouldn’t that cause a delay in getting injured personnel necessary medical treatment?” Carson asked.

John nodded. “That is a concern but as we saw today we also have to be concerned with keeping the city safe and secure as a whole.”

Elizabeth nodded. “It’s a good suggestion and one that we should consider and discuss in more detail. Any other ideas?”

A few more suggestions were made, though most of Rodney’s mind had by that point returned to thinking about the orb. Finally, he heard Elizabeth thanking everyone for their contributions.

He made to rise from his seat as she dismissed them.

John, Rodney, could you two stay a moment?”

Rodney fell back into his seat. He felt John tense beside him. Now what?

Once the door closed behind the others Elizabeth turned to face them. “Thank you for your actions today,” she started. “You likely saved the whole city, and prevented the Wraith from learning about our continued survival.”

John started to relax. “You’re welcome but no thanks are necessary. We couldn’t let the Wraith loose in the city.”

I know.” Elizabeth sighed then continued. “The thing is that you broke into areas you were restricted from to do it. And you didn’t wait for backup.” She held up her hand. “I know, extenuating circumstances and all, I understand, believe me, I do. But did you even consider trying to contact anyone else?”

There was no time, the Wraith were getting closer to accessing the mainframe with every moment we delayed. We couldn’t take the risk that they would be able to get a signal out if we waited any longer,” Rodney told her. “Plus at the time we had no idea if we were the only ones still awake and moving. There was no way to know how far the stun effects had reached.”

I know, I’m not faulting you. It’s just that the Daedalus left Earth two days ago with the delegation from the IOA. I’m sure that this incident is going to be included in their review once they learn about it. While I don’t know who else has been sent, one of the members is Richard Woolsey who is a stickler for rules and protocol. While I can see how necessary your actions were, I’m not sure how he or the rest of the delegation will see it. So I want you to think of your responses now before they get here to ask.”

Great.” Rodney sighed. It looked like their fates would be getting decided soon.

Elizabeth raised an eyebrow, then continued. “I’m also a bit concerned myself about how easily you were able to get around the security protocols.”

Rodney waved her off. “Come on, I designed that system. And I’m the expert on the Atlantis systems it ties into. You don’t have to worry about anyone else being able to break in.”

She shook her head. “While I’m glad to hear that no one else could get through it so easily, there is still the concern that you could.”

What? Why?” Rodney asked confusedly.

John sighed. “Because we’re still considered compromised McKay. What if our intentions hadn’t been good?”

Oh. Well, I don’t see what you can do in that case. I mean, you could have someone try to update the system but I doubt there’s anything you can do that I wouldn’t be able to get through quickly.”

Elizabeth shook her head in exasperation but a fond smile was tugging at her lips. “Not exactly what I wanted to hear. I would suggest that you not say that to the IOA once they arrive.” She waved her hand to the door. “Go on, get out of here.”

Rodney stood immediately, glad to finally be getting out of the conference room. John was a moment behind him. They headed for the door.

And gentlemen?” Elizabeth called after them, causing them to stop and look at her. “Thank you again.” She nodded at them and they nodded back.

Well, I should get to the lab,” Rodney said as they headed to the transporter. “I’ve got so many ideas about how that orb was able to amplify the stunner.”

John cleared his throat and Rodney turned to look at him. “It’s late McKay. The lab will still be there tomorrow. Let’s get dinner and then go to bed.”

Rodney frowned but then his stomach gave a growl. “I suppose I should eat first but I’ve got too many ideas running through my head, I won’t be able to sleep.”

John raised an eyebrow. “I said we should go to bed, I didn’t say anything about sleeping yet,” he pointed out.

Oh. Oh!” Rodney’s eyes widened and he felt himself start to flush. He still wasn’t used to this. “In that case, I guess the lab can wait until morning.”

Good,” John said, ushering him toward the transporter. “I’ve got plans.”

Rodney had a feeling he was really going to enjoy those plans and he found himself looking forward to it.

Chapter Text

John shifted nervously as he waited near the entrance steps to the Control room. He and Rodney had been called here by Elizabeth with the news that the Daedalus was entering the system and would be here within the hour. Now the ship was just moments away and here he and Rodney stood, waiting to meet those who would decide their fate.

Calm down,” Rodney said from beside him. “Before you make me nervous, and that is not something we want to happen.”

John knew he was right but he couldn’t help it. “This is our lives at stake,” he hissed to Rodney.

They need us too much,” Rodney said, his words full of his usual arrogance, yet his tone relayed the same doubt that John was feeling. “We just need to convince them of that.”

A bright flash of light filled the center of the Gate room and when it faded there was a group of people standing there. John snapped to attention then saluted when he spotted General O’Neill at the front of the group. Even as he saluted, he felt a surge of hope. While he’d never served with or under O’Neill, everything he had heard and seen of the man made him respect him, a feeling he didn’t often feel for his superior officers. He could only hope the man’s presence was a good sign.

At ease,” O’Neill said, returning the salute. “Colonel Sheppard, you’re looking a bit different since I last saw you. Did you do something new with your hair?”

Rodney snorted. “Like he can do anything with those cowlicks,” he muttered.

O’Neill turned to him then. “McKay,” he said. “You’re looking a bit-”

Rodney cut him off, glaring. “Okay, fine, let’s get it over with. I’m what? Blue? Smurf-like? You can’t say anything I haven’t heard in the last few weeks.”

O’Neill’s eyebrows rose. “I was going to say grumpy but I get the feeling that’s your normal state.”

Rodney started to retort and John took the chance to shift his weight and step on his foot, receiving a glare. ‘Knock it off, we need him on our side,’ he tried to communicate with his eyes.

Rodney huffed and fell silent, so the message must have been received.

My God,” one of the suit wearing men behind O’Neill said in a British accent as he stopped looking around the Gate room in awe to stare at them. “I’d read the reports but still, to see such a change. Are you even still human?”

John bristled at his words and tone but held his tongue, and surreptitiously grabbed Rodney’s arm to keep him from saying anything either.

O’Neill turned and gave the other man a look that shut him up. John took the opportunity to study the others in the group. The lone woman was of Asian descent, looking around the room with a look of awe. There was a second man in a suit, balding, who reminded John of the EMH from Star Trek. Another man, dark-skinned, bald and wearing a military uniform with the rank of full bird Colonel rounded out the group. At least until John spotted one more person standing behind everyone else. Colonel Caldwell had returned to Atlantis. His heart sank. Well, it’s not like he really expected to retain his command.

So, I think introductions are in order,” O’Neill stated.

That would be nice,” Elizabeth said as she joined them.

Liz! So good to see you,” O’Neill greeted her.

She gave him a diplomatic smile. “It’s wonderful to see you again as well General, though I wish the circumstances were better.” She looked at the group with him. “Dr. Jackson didn’t come with you?” she asked curiously.

Yeah, well you know how it is. He wanted to but was needed on Earth.” O’Neill winced slightly.

Elizabeth’s smile became a bit more genuine. “He gave you hell for leaving him behind, didn’t he?”

Excuse me,” the balding man in the suit interrupted. “I believe introductions were mentioned?” He turned to Elizabeth and held out his hand. “Dr. Weir, it’s good to meet you. Richard Woolsey.”

Mr. Woolsey,” she greeted him. “And of course this is Colonel Sheppard and Dr. McKay.”

Yes, nice to meet you gentleman as well,” Woolsey said and with only a brief hesitation he shook their hands as well.

John’s estimation of the man went up slightly at that, especially when none of the others made a move to do the same.

Also with us are Russel Chapman the British representative for the IOA,” he indicated the rude suit-wearing man, “Camile Wray,” the lone woman, “and Colonel Abraham Ellis. You are of course familiar with Colonel Stephen Caldwell.”

Yes, of course.” Elizabeth gave Caldwell a small but genuine smile. “Colonel you are looking much better than the last time we saw you.”

Yes, I’m feeling much more myself these days,” he told her.

Elizabeth nodded at him, then turned to the group as a whole. “I know you had a long trip here and would probably like to get settled in. Let me show you to the quarters we’ve arranged for you.”

Woolsey glanced at the rest of the group then nodded to her. “Yes, that would be nice. Thank you.”

John and Rodney watched them go, not missing the looks of disgust that passed over both Ellis’ and Chapman’s faces as they passed them. If their reactions were anything to go by then things were not looking good for the two of them. He only hoped that the others would be more inclined to act in their favor.

Once the delegation had left the Gate room, John started to lead Rodney out as well since they were still restricted without an escort.

Colonel Sheppard, Dr. McKay, I was wondering if I might have a word with the two of you?” Caldwell called after them.

Rodney stiffened but John quelled him with a look. “Sure,” he drawled out, forcing his body to stay relaxed. “Here?”

Somewhere a little more private. The conference room?” Caldwell suggested.

John shrugged. “Fine by me.” He led the way.

Once the doors had closed behind them, Rodney crossed his arms over his chest. “What do you want?”

Caldwell stiffened slightly, his body automatically falling into parade rest. “I would like to apologize to both of you for my previous actions.”

You mean when you tried to kill Sheppard, nearly killing me in the process?” Rodney snapped.

Rodney,” John said, reaching out to grip his shoulder. When he fell silent he turned back to Caldwell. “It wasn’t your fault.”

Rodney huffed in disagreement but otherwise kept quiet.

Still, I feel responsible even though it was the Goa’uld that actually gave those orders and carried out those actions.” He took a deep breath. “I thought I should explain his reasoning, at least as far as I understand it.”

A look of curiosity passed over Rodney’s face but it was clear he didn’t want to ask. So John did. “And?”

It was a minor Goa’uld working for Ba’al. His agents managed to snatch and implant me just before we left on our last trip out here. His orders were to either find a way to gain complete control of the city or destroy it to prevent the Wraith from reaching the Milky Way.”

So when I was infected with the retrovirus?” John started to ask.

The Goa’uld determined it was the perfect opportunity for it to take control, first of the military and then the rest of the city. Especially once you escaped confinement, it saw it as an opportunity to permanently eliminate a threat to its power.”

So you admit to trying to kill him!” Rodney exclaimed.

Rodney!” At the scientist’s hurt look, John softened his tone. “It was the Goa’uld, not Caldwell.” He turned back to the Colonel. “Thank you for the explanation. What happened wasn’t your fault and I don’t blame you. Still, if you need to hear it then I accept your apology.”

Thank you,” Caldwell said. He hesitated a moment then went on. “Just to be clear, I would have authorized lethal force in that instance but only as a last resort and only because you had already attacked Dr. Weir and the men guarding you.”

John felt Rodney bristling beside him and spoke first to ward him off. “And I appreciate that. I would have made the same call.”

Rodney’s eyes widened. “What?! How can you-”

John shook his head. “Rodney. How do you think I would feel if I had seriously hurt or, worse, killed someone? Why do you think I insisted on armed guards being stationed outside my door?”


It didn’t come to that. Let’s just put it behind us, alright?”

Rodney’s expressive face showed his conflict. Finally, he sighed. “Alright, fine.”

Dr. McKay, I am also sorry for the actions that led to your injury and infection.”

Rodney frowned at Caldwell, glanced at John and stubbornly kept his mouth shut while he thought about everything that had been said. “Alright, fine. It’s not your fault, you’re forgiven,” he finally said, if a bit petulantly.

So I guess you’ll likely be taking command then?” John asked, trying to sound nonchalant and failing.

Caldwell gave him an odd look, his face momentarily softening in realization. “No, even if they were to offer it to me I wouldn’t take it. I’m happy to stay in command of the Daedalus.”

But-but-but you wanted the post! You’ve been trying to get it since we got back in contact with Earth!” Rodney burst out in disbelief.

I did. But if recent experiences have taught me anything it’s to be happy with where I am. Besides,” he started, turning to look at John. “You have an unorthodox approach to command, and while I still think you have a lot to learn as you lack either training or experience in certain areas, my brief time in this galaxy has shown me that an unorthodox approach is just what is needed. You have the respect of your men and have built a rapport with both the civilian members of this expedition and the locals, something that is definitely needed with the threat of the Wraith. If I had any say about it I’d recommend they keep you, if not in your current position then as a liaison.”

Wait, you’re on our side?” Rodney asked incredulously.

John too was having trouble believing his ears. Not only was Caldwell, a superior officer John was sure viewed him with contempt, offering him praise, but he was also supporting him remaining on Atlantis when in the past he would have been the first trying to get him removed.

Dr. McKay,” Caldwell started as he turned to face the astrophysicist. “You are arrogant, condescending, rude and one of the most irritating men I have ever met. And yet you are also one of the most brilliant and, despite your attitude and pessimism, you have also shown you are dependable and brave when necessary. This mission needs people like you, like the both of you.”

A flush spread across Rodney’s face as Caldwell spoke. He opened and closed his mouth repeatedly, no words coming out.

Thank you, Colonel,” John said.

Rodney snapped out of his daze. “Yes, thank you.”

Caldwell simply nodded.

John hesitated, then decided he might as well go for it. “So if you’re not here to take over command, do you have any idea how the delegation might be leaning?”

Caldwell looked uncomfortable. He sighed. “I admit it doesn’t look too good for you Sheppard.”

I didn’t think it did.”

I believe General O’Neill will do everything he can for you but I’m not sure how much pull he’ll have. Your best chance would be to convince some of the others that you’re necessary here and not a threat or hindrance.”

Can you tell us anything about what to expect from them?”

Your best bet is Woolsey, followed by Wray. They are the two more likely to be open-minded. I hate to say it but Chapman and Colonel Ellis have likely already made up their minds.”

Yeah, I got that impression earlier,” John admitted.

Caldwell nodded. “I feel I should warn you that Ellis is likely here because he wants the command. He believes the military should be in charge of this base, not the civilians and, if he succeeds, he will likely try to have the entire command staff replaced.”

Great, another military goon who wants to come in and take over with no concept of how things work here,” Rodney grumbled.

Seeing that Caldwell had said all he was going to say on the matter, John straightened up. “Thank you for the information Colonel, we really appreciate it.”

Caldwell nodded. “And thank you for your time.” He turned and exited.

John glanced at Rodney. “Come on, let’s go get something to eat.” He led him from the room, nodding to the men who escorted them to the Gate room door. They entered the transporter and John selected the destination outside the Mess.

Everyone they passed nodded greetings to them. John had noticed a big improvement in the attitudes concerning them after the Wraith attack, particularly in regards to Rodney. Just about every interaction since then was filled with respect for the two of them. He shook his head. Rodney still didn’t understand the looks he’d been receiving from most of the military, especially those who had been in the control room.

They entered the Mess to discover that Elizabeth must have decided to give the delegation a tour of the facilities as they passed them on the way to the food line. John’s hands clenched on his tray as his enhanced hearing heard Chapman’s comment of disgust about them contaminating the food and Ellis’ question about where their guards were.

He glanced back in time to see Elizabeth’s strained diplomatic face and the furious look on General O’Neill’s face. At least Woolsey and Wray looked uncomfortable about the remarks.  That was something.

Rodney was bristling beside him, so John nudged him. “Come on,” he said, leading him toward a table in the back.

John was glad when the delegation finally moved on from the Mess, noting that the tension in the room eased rapidly once they had gone. He turned to Rodney who still looked unsettled. “So what’s new in the labs?”

Rodney rolled his eyes and shot him a look that said he knew what John was doing but began talking anyway, launching into an account about the latest screw-up from the newest batch of scientists sent by the SGC. John grinned as the tension left Rodney’s shoulders.

They had nearly finished their meal when Teyla strode up to the table. “John, Rodney, may I speak with you?”

Sure, have a seat,” John told her.

Thank you,” she said as she sat. She took a deep breath. “I feel I must apologize to the both of you. I know that our recent interactions have been strained lately and that the fault for that lies with me.”

John gave her a startled glance, then exchanged a look with Rodney. First Caldwell, now Teyla apologizing? “I don’t think you have anything to be sorry about,” he told her.

Yes, I do,” she said as she met his gaze. “I know I led you to believe that it was your actions that made me uncomfortable but that is not the case. I meant what I said when I told you that you were not yourself and to think nothing further of that day.”

Rodney stared at her confused, then gave John a suspicious look. Great, he should have told Rodney about this earlier, now it would look like he’d been hiding something.

Teyla continued. “It was not your actions that made me uncomfortable. It was the change in your appearances. You must understand that apart from the Wraith we here in Pegasus have only encountered other humans. I know that you are both still the people I have grown to know so well and care for but I had to reconcile that with your new appearances. Something I admit to struggling with.”

She glanced down at the table. “I saw how you had physically changed and I flinched away. Not because you appear similar to the Wraith, as you do not. But because that is the only reference for different that I had.” She lifted her eyes to look at them again. “Also I fear that your change brought up worries of my own about my having the gift to sense the Wraith. I have told you of my nightmares, of the Wraith DNA I carry taking over. I saw your physical change and though mentally you are yourselves, I saw my nightmare come to life in the two of you.” She took another deep breath and glanced between the two of them. “So I apologize for my behavior and hope I have not damaged our friendship.”

John shook his head. “You had a perfectly reasonable reaction,” he told her. “You’re not the only one who had a hard time adjusting to our new appearances, even we find it difficult at times. It’s not a problem.”

But Rodney was looking at her thoughtfully. “Why now?” he asked. “It’s been weeks. I can understand taking time to get used to the new us. But why the sudden need to apologize?”

Teyla met his gaze calmly. “I am ashamed to say it took my overhearing the negative words of our visitors. I became angry at their words. What right did they have to say such things about two of the bravest men I have had the privilege to know and call a friend? And then came my realization, for how was I any better if I could not look past your appearances either?”

Rodney nodded. “Apology accepted.”

Thank you, my friends,” Teyla said, bowing her head. She stood and looked at them a moment, causing them to also rise. “I shall see you in the morning,” she said, then leaned forward to touch foreheads with first John, then Rodney. Then she gave them a smile and left.

John blew out a breath. “Okay, I don’t know how much more of these serious conversations I can take. Too much emotion involved. Let’s get out of here before someone else decides they need to have a heart to heart and apologize.” He glanced at Rodney, expecting to get an agreement only to find the Canadian staring at him. “What?”

What was Teyla talking about earlier? What actions did you think made her uncomfortable?”

Shit. John had forgotten that part of the conversation. “Not here.”

Rodney nodded. “Fine. Let’s go.”

And here John had been hoping they were done with serious conversations for the day. As he followed Rodney to his quarters he could only hope that he wasn’t about to lose the only person that made things bearable these days.


Rodney glanced at John as he led him through the corridors to his quarters. The man looked like someone on their way to the executioner. His heart sank as his mind thought up all the possible things John might have done and why he wouldn’t want to tell Rodney.

Thankfully they reached Rodney’s quarters before his mind could really go into detail on what John might say. He opened the door with a thought, something that still gave him a thrill, and gestured John inside. Once the door closed behind them he crossed his arms over his chest, a defensive habit he couldn’t seem to rid himself of, and stared calmly at John. “So talk.”

John took a breath and ran his hands through his hair. “You have to understand, this was back when the retrovirus was first starting to affect me, before we knew it was affecting me and before I was put on the inhibitor.” He began to pace. “Teyla and I were sparring. And for once I was winning. And with the retrovirus running through my system I felt invincible. I managed to corner her against the wall and then the adrenaline rush kicked in and things got out of hand.”

Rodney’s heart sank as he pictured it, putting together what John wasn’t saying. “You slept with her.” Not that he could really blame him, Teyla is gorgeous. And it’s not like they were together at that point so it wasn’t a betrayal. So why was Rodney feeling so bad at the thought? Why was John acting so guilty? Unless he was just settling with Rodney and he really wanted Teyla, and now he might have a chance with her. Was Rodney about to be dumped? It wouldn’t be the first time someone left him for someone better.

What? No! I just kissed her,” John exclaimed, oblivious to the path Rodney’s thoughts had taken.

Relief filled Rodney. It was only a kiss. “Oh,” he said, then frowned. “Then why the secrecy? Why are you acting guilty?”

I didn’t mean to keep it secret. You know how I am about personal things.”

You mean how you don’t talk about them.”

Exactly!” John nodded. “Anyway, I didn’t remember at first. And when I did I apologized to Teyla, since I kinda assaulted her. And then she was acting distant, so I thought I had ruined our friendship, and I just didn’t know how to bring it up.”

But you didn’t, we got that all settled earlier.” Rodney was still feeling off kilter. “So you kissed Teyla. Not that I can blame you, she’s gorgeous. But does that mean that some part of you wants to be with her?”

John must have finally clued in on Rodney’s earlier thoughts. “Hey, yes I kissed her but it didn’t mean anything. I told you, it was the retrovirus and the adrenaline and she was right there. Yes, Teyla is gorgeous but she’s not the one I want to be with.” He gently cupped Rodney’s face. “I’m happy where I am.”

Are you? Or are you just settling because you don’t think anyone else would want you?” Rodney couldn’t meet his eyes as he asked, too afraid of what he might see there.

What? Of course not!” John frowned at him. “Why would you ask that? Unless that’s the way you feel? About me, I mean?”

No! It’s just, even like this you’re gorgeous, and you’re smart, brave, athletic and I’m, well, I’m me. I just don’t see how anyone, let alone someone like you could want someone like me.” He gestured at his body.

Someone who is brave when he needs to be, the smartest man I have ever met, has a good sense of humor, likes a lot of the same things I do, and has the most beautiful blue eyes I have ever seen as well as the best ass.” John raised an eyebrow at him.

Oh, well when you put it that way.” A surge of pleasure went through him at John’s words.

John shook his head, fond exasperation evident in his expression. “Yes, I put it that way. Now, are we done with the emotional talk? I think I’m over my quota for the year.”

Rodney snorted. “Yes, yes we’re done.”

Good,” John said and leaned forward to kiss him.

Rodney’s eyes closed as he enjoyed the kiss. But as John’s hands started to wander a thought hit him and he placed his hands on John’s chest and gently pushed. “Wait, wait.”

Rodney?” John asked as he pulled back.

You should go,” Rodney told him.

His face fell. “I thought we’d settled this, I want to be here, with you.” He frowned. “Unless you’re still upset about that kiss.”

No, it’s not that,” Rodney tried to reassure him. “It’s just, the delegation is here. You can’t afford to do anything that would give them cause to get rid of you. We already have an uphill fight on our hands.”

John’s face became determined at the reminder. “I don’t care. I’m probably going to lose my command and my commission either way but I won’t put up with losing you too.”


Rodney, you’re the only thing that’s made life bearable since this mess started. I am not going to lose you. And if the delegation doesn’t like it they can kiss my blue, scaly ass.”

I’m the only one allowed to look at, let alone kiss your ass,” Rodney told him with a frown.

John smirked at him. “Well then, I guess I have to stay or my ass will feel neglected.”

Rodney rolled his eyes as he felt his resolve to make John leave crumble. “Yes, fine, stay.”

Good, I will,” John said, and kissed him again, hands deftly making short work of various articles of clothing.

Rodney groaned into the kiss. Why had he wanted John to leave anyway? He should just stay here permanently. Yes, that was a good plan. He would tell John that plan. Later, when his brain wasn’t being turned to mush by John’s talented hands and mouth. “John,” he moaned out as that beautiful, wicked mouth worked it’s way down his chest.

Shh, I’ve got you.”

Later, as they lay tangled together in the afterglow, Rodney poked a finger into John’s chest. “Well if you’re going to throw away what little career you have left for this, then you might as well just stay permanently.”

John’s face lit up. “Why Rodney, are you asking me to move in with you?”

I guess I am.”

Then I guess the answer is yes,” John told him. “And I’m not throwing anything away, I’m just deciding what is more important,” he said as he tightened his arms around Rodney.

Rodney made a happy sound at his words and started to drift off, tightening his own arms around John in return. Tomorrow the fight to stay in their home would begin but for now, this moment in time, everything was right in his world.

Chapter Text

John was in a good mood as he headed to his quarters early in the morning. He and Rodney had settled their relationship the night before, laying Rodney’s doubts to rest, hopefully for the last time. And Rodney had even asked him, well more like told him, to move in with him. They would be meeting for breakfast before they had to meet with the delegation but first, he needed to change. It wouldn’t do to meet with the delegation in yesterday’s uniform. It was early enough he might even have time for a short run or workout though that would necessitate another shower, sadly without Rodney this time. He smirked at that memory.

His smirk faded as he rounded the corner to his quarters and came face to face with General O’Neill. “Sir!” he said as he came to a halt. “I was just-”

O’Neill’s sharp eyes seemed to take everything onboard in one glance. “Save it Sheppard. I’m not asking.”

John felt a surge of relief. “Then did you need me for something? I didn’t receive a call from the Control room.” He reached up and checked his earpiece, ensuring it was on and working.

Nah, just taking a stroll around this city of yours.” But the General’s face belied his words. “I’m sure you know it best. Walk with me, show me around.”

John hesitated, glancing down at his uniform.

I’m sure it won’t take us long, you’ll have plenty of time to change.”

Of course, Sir.” John led him to the transporter. “I take it you’d like this walk to be peaceful? Private?”

O’Neill pointed at him. “Smart man.”

John nodded and selected the East Pier.

Hmm, nice view,” O’Neill said as he looked around, turning to look back at the city and then out across the water. He walked toward the end of the pier. “How’s the fishing?” he asked, hands in his pockets as he leaned against the railing.

You didn’t want to come out here to discuss the fishing,” John told him, wanting to get this conversation over with.

O’Neill raised an eyebrow. “You chose the location.”

John just stared at him blankly.

The General sighed. “Look, I like you Sheppard. You remind me of myself and you’re a damn fine pilot. And I think you’ve managed to do a pretty good job out here with what you had available.”

Thank you, Sir.”

But you’ve gotten yourself into quite the situation.” He waved a hand to silence John. “Granted, this isn’t your fault,” he gestured at John. “Except in the way that it is.”

John frowned at him. “Sir?”

Why haven’t you pushed for more control of the city?”

Dr. Weir is the leader of the expedition,” John pointed out.

O’Neill shot him an incredulous look. “You do know that the moment you encountered the Wraith you would have been justified in taking command of the expedition. Once you encountered such a dangerous enemy you were thrust into a military situation.”

John shifted uncomfortably. “Elizabeth- Dr. Weir made it clear that she determines what is a military situation.”

Fer crying out loud,” O’Neill groaned as he slumped against the railing. “No wonder she pushed so hard to keep you as the military commander,” he muttered quietly, obviously not intending John to hear.

But he did and he stiffened as he fought to control his emotions. Oh, he had suspected but it was one thing to suspect and another to have confirmation. Plus Elizabeth might have implied a thing or two without really saying anything.

He must not have done a good job of hiding his reaction because O’Neill noticed. “Shit, I’m really screwing this up.” He sighed. “Look, that’s not why you were promoted or given this command.”

John eyed him, not really believing him. “It’s not?” he asked blankly.

It was definitely considered but it was actually a point against you,” O’Neill told him. “Look, you all came back for your debriefing and we received report after report from the scientists about how necessary it was for you to remain out here. That, despite others having the gene, the city worked better when you were around. And it was obvious that you wanted to return, so unless you suddenly objected you were going to be sent back here. But that presented a problem as you weren’t really qualified to be the Military Commander.”

Which is why they were going to give the job to Colonel Caldwell.” Something else John had suspected.

But that would have had led to other problems. You see, you had done the job for over a year, you had earned the respect and loyalty of the men out here. Military and civilian alike. That data burst we received? Multiple reports praising you for your efforts keep them alive in a tough situation.”

John stared at him, stunned. “Even though it’s my fault we were in that situation? Even though I woke the Wraith.”

Nobody blamed you for that.” O’Neill grimaced. “Almost nobody, there was one little weasel I’d rather never deal with again. Most understood it was beyond your control and thought you did the right thing in going after those men. Made them realize you would go after them in the same situation.”

John nodded. “We don’t leave our people behind.”

Exactly,” O’Neill agreed. “But that left us in a bit of a tight spot. You were obviously needed on the city according to all reports. But after leading the military for over a year and earning their respect and loyalty it would be difficult for them to easily accept another CO, especially with you right there. A difficult position to put any commander in. And if there was a conflict between the two of you? A difficult position to put the men in.”

And I was promoted avoid such a situation.”

Don’t get me wrong Sheppard, you earned that promotion. True, you could do with some more polishing. You might want to brush up on some of the literature available,” O’Neill added with a pointed look.

John grimaced but nodded. He hated the paperwork involved but he owed it to his men, especially after the loyalty they had apparently already shown him. Then again, it might be a moot point. He said as much to the General.

The older man nodded. “Yeah, I can’t promise you how things will turn out. Officially I’m neutral at this point. Unofficially I don’t think this affects your ability to command.”

Thank you, Sir. It’s good to know that someone’s on my side, at least unofficially.” John paused and thought back over the conversation. “But what did you mean about Elizabeth being a point against my promotion?”

O’Neill sighed again. “I like her, don’t get me wrong. But she’s a diplomat and should not be in charge of a situation like this. She’s going to want to look for peaceful solutions first, not necessarily a bad thing but can you honestly tell me the Wraith could be negotiated with?”

No!” John replied vehemently.

And that’s why we were leaning toward a more military expedition before we sent you back out here. There was talk of replacing her.”

John stared at him in shock. “But you didn’t.”

No, it was decided that it was better to keep the leadership intact as you had the knowledge of how things worked out here. We’d already seen what happens when someone who doesn’t know the lay of the land tries to take command.”

John winced at the reminder of Colonel Everett’s fate.

Anyway, she knew that there had been discussions of removing her from command. She obviously realized that a new Military Commander could push for that to happen. So it was in her own self-interest to push to retain the one she already had, one she had reason to believe she could control.”

John furrowed his brow at that. “Control me?”

O’Neil shrugged. “Most thought she was controlling you through sex.” He shrugged again when John grimaced. “Not me. Aht! Still not asking!” He shook his head. “But let me guess, she let you believe it was her efforts that secured your promotion?”

John grimaced. “She might have implied it,” he admitted.

She might even think it’s true. But it’s not.” O’Neill glanced at his watch. “It’s getting late, we need to wrap this up if you want to have time to change and grab something to eat. But think about what I’ve said. And remember, Weir doesn’t have the necessary knowledge to know when something is a military situation.”

John grimaced as he recalled his earlier words.

O’Neill nodded as he saw his point hit home. “So you had better think about what kind of CO you’ll be if things go your way. Because that’s who you have to show the delegation if you want them to get behind you.”

Thank you, Sir, you’ve given me a lot to think about,” John told him honestly as he led the General back to the transporter.

Good. Now seriously, how’s the fishing out here?”

John didn’t pay much attention to General O’Neill extolling the benefits of fishing before they parted and he headed back to his quarters. He had just enough time to change and get to the Mess for something quick to eat before he had to meet the delegation.

There you are! It’s about time,” Rodney greeted him with a frown as he joined him at a table. “I expected you here a while ago.”

Yeah, I ran into General O’Neill earlier and he wanted to see more of the city. I ended up showing him the East pier.”

Rodney shot him a sharp look. “Oh? And did he say anything?”

John shrugged and tried to look relaxed. “He kept asking about how the fishing was.” This wasn’t the place to talk about everything O’Neill had said. He tried to convey that to Rodney with his eyes. Besides, he still needed to wrap his mind around everything himself.

Rodney gave him another sharp look before nodding. They would be speaking about it later. “Well hurry up, we don’t have a lot of time.”

A glance at his watch confirmed Rodney’s statement and John bolted down his food quickly before they both returned their trays and headed for the doors. It could be John’s imagination but it seemed like everyone they passed was giving them encouraging looks as they made their way to the conference room. He thought about O’Neill’s words; about how he had earned their respect and loyalty and decided maybe he wasn’t imagining it. Then they were at the conference room and John took a deep breath to steel his nerves before entering.

John settled into his seat in the conference room and resisted the urge to slouch. General O’Neill’s earlier words still rang in his ears and he knew that it was important he presented the right image.

The delegation from Earth was seated on the other side of the table. He eyed them, trying to figure out the dynamics of the group. Woolsey was in the center, obviously the one in charge of the proceedings, with a stack of closed files in front of him. To his right was General O’Neill, looking bored. On O’Neill’s other side was Colonel Ellis. Chapman sat on Woolsey’s left, with Wray on his other side. So military on one side, civilians on the other? He frowned slightly as he took in Elizabeth seated on one end of the table. He wondered why she was so far away.

Rodney began to fidget slightly in his seat beside John. He recognized the expression on the scientist’s face. His hands were itching for a computer to do some work on. John gave him a look to settle him down.

Glancing down the table John met Elizabeth’s calm gaze and received a nod back. She stood to lose a great deal here as well if the delegation’s decision was unfavorable.

At that moment the doors swung open allowing Carson entrance. “I’m sorry I’m late,” he apologized. “I was with a patient.”

Apology accepted Dr. Beckett, that is a perfectly understandable excuse. Please be seated,” Woolsey told him, gesturing to a seat at the other end of the table from Elizabeth.

John resisted the urge to frown. He and Rodney were in the middle of their side of the table Carson and Elizabeth were seated at the opposite ends. It left him feeling like he was on trial.

Thank you all for joining us today,” Woolsey began as he clasped his hands together on top of his files. “I believe we all know the reason for this meeting but I will state it for the record. We are here to investigate the decisions that led to Lt. Colonel Sheppard and subsequently Dr. McKay being infected with an untested Iratus retrovirus, as well as to decide if Colonel Sheppard and Dr. McKay are still capable of performing their duties and, in the event that they are not, then what should be done with them.”

John did not like how that last part sounded. It seemed…ominous.

Now, we’ve all read the reports but I would like to hear how this happened in your own words. Colonel Sheppard, if you would please start with your arrival on the planet.”

And so they began to recount, again, the events that led up to their present circumstances. It wouldn’t have been so bad if it weren’t for the constant interruptions and questions. Questions about every decision made on the planet.

When you learned of the presence of a Wraith, why did you stay and decide to seek it out? Why didn’t you just leave?” Chapman asked.

Because the Wraith had been killing villagers for years. We had the ability to put a stop to that. It was the right thing to do.” John glared at him. “If you need more than that, you can consider it an act of goodwill toward a possible trading partner.”

And what did you expect to trade for?”

While we are now able to contact Earth and are receiving regular shipments of supplies, there are times it is necessary to trade for food,” Elizabeth answered.

Hmm,” Woolsey said, writing something down on a notepad. “Continue, please.”

The next interruption was about bringing Beckett to the planet. “Was it really necessary for Dr. Beckett to go? Couldn’t someone else have taken the requested samples?” Wray asked.

Yes, it would have been simple to show someone else how to collect the samples but it was an unprecedented opportunity to interact with a Wraith that didn’t see us as food. And if Zaddik’s drug worked as he said, I needed to discuss it with him, see the process used to create it,” Carson answered.

But the drug didn’t work as he said, isn’t that right Doctor?” Ellis asked.

Aye, as far we can tell there is nothing in the drug that would affect a Wraith’s need to feed.”

Wray raised an eyebrow. “And yet this Zaddik claimed that the young Wraith, Ellia, didn’t feed.”

Carson sighed. “At this point it looks like Ellia let him believe the drug worked and kept him in the dark about her feeding habits.”

So she misled this Zaddik, and consequently the rest of you?”

It looks that way, but at the time we had every reason to believe Zaddik when he said the drug worked.”

Hmm,” Woolsey said. “Dr. Beckett, once your request to travel to the planet was approved, what did you pack to bring with you?”

My medical kit, of course, including the equipment needed to collect samples from Ellia. A few tools to do some simple analysis of Zaddik’s drug.” Carson sighed. “And a sample of the Iratus retrovirus that I had been working on.”

Forgive me if I’m wrong, but wasn’t this retrovirus experimental and untested? Still being refined?” Ellis asked.

Yes,” Carson said.

Then why the hell did you think it was a good idea to bring it with you? Unless you were planning to use it on this Ellia all along?” O’Neill questioned

No! I had no plans to test it. I’m not even sure why I brought it other than I was an idiot and wanted to have it on hand to test against Ellia’s samples. I take full responsibility for my mistake.”

And you Dr. McKay, were you aware that Dr. Beckett had brought the retrovirus with him?” Woolsey asked.

Rodney frowned. “As I was another planet at the time, no I was not aware of that decision.”

But you were aware that the retrovirus existed, weren’t you? After all, as the Chief Science Officer of this expedition, all scientific research must be approved by you,” Woolsey stated.

Rodney shifted uncomfortably. “I was vaguely aware that Carson and several other medical personnel were working on such a project.”

Then you weren’t aware that they had proceeded to a point where they were looking to test their retrovirus?”


And what about after Dr. Beckett arrived. When did you learn that he had brought the retrovirus with him?” Woolsey continued to press.

Not until after Ellia had already taken it,” Rodney admitted.

As head of the science department, you should have known what was being researched and how far it had progressed. Dr. Beckett should have informed you when he brought the retrovirus with him,” Wray said with an irritated glance at Carson. “But if you had been following up like your position requires you might have suspected that he had brought the retrovirus along.”

John’s hands clenched beneath the table. He didn’t like how accusatory they were sounding toward Rodney. None of this was Rodney’s fault.

I suppose I should have been more aware but do you have any idea what I’m dealing with here?” Rodney began, his words picking up speed as he started on one of his typical rants. “You keep sending me these supposed experts and yet I spend most of my time making sure that they’re not blowing up the city. We tell them not to touch something, not to activate something, and what do they do? They touch, they activate.”

Isn’t it their job to study the Ancient technology?” Chapman asked.

Yes, study but not blindly. Last week one of the electrical engineers decided they knew better than both Zelenka and me, and ended up in the infirmary when he tried to bypass a system after we warned him not to because of the secondary relays. These scientists are brilliant in their fields but they don’t know Ancient systems and when they try to apply what they do know to Ancient technology we run into issues.” He sighed. “So yes, I may have let some things slip by because I didn’t view them as being as important as keeping the city intact.”

You mean because you don’t view them as a real science,” Wray countered. “We have heard reports of your belief that the so-called soft sciences, including medicine, are not real sciences. If you are so dismissive of things you feel are beneath your notice then how are we to believe you are capable of fulfilling all of your duties? Why should you remain the CSO?”

Rodney began to flush. “Er, well, yes, I may have said something to that effect. But,” he began, his hands waving in emphasis, “that doesn’t mean I don’t pay attention. I still read the reports from the botanists, the chemists, etc. I follow up with them when I have time. I just prioritize the things that are more likely to kill us all. For example, on the one hand, Dr. Parrish in botany is working on some plant hybrid that he hopes will be able to absorb various forms of radiation and filter it from the environment. Now as someone who has been exposed to an excessive amount of radiation for one lifetime I can see the value in this project. But on the other hand, Dr. Simpson is working on trying to replicate the process of creating drones, working with highly volatile equipment. Which of these is more dangerous and thus requires more attention?”

Woolsey nodded thoughtfully. “A good point. But I would think that you would also prioritize something like the retrovirus since, if it worked, it would be an effective method of dealing with the threat of the Wraith.”

Rodney sighed again. “Look, I admit that biology and medicine is not my strong point. While the research into the retrovirus is technically scientific research,” and Rodney looked pained to have to admit that, “it mainly falls under medicine. And we have a Chief Medical Officer for a reason. As much as it pains me to say it, Carson understands his field much better than I do. So yes, I trusted that he knew what he was doing, while I focused on other matters.”

Carson looked touched and a bit smug at Rodney’s words. John knew he would be rubbing them in the next time Rodney ended up in the infirmary and called medicine voodoo.

Hmm.” Woolsey made another notation and glanced at the rest of the delegation. “Let’s continue shall we?”

And so they went through the rest of the mission. Thankfully with fewer interruptions. But then they reached the part where Ellia attacked John before he and Ronon managed to kill her.

And what did you do with the body?”

John frowned. “Well Dr. Beckett retrieved some samples but the villagers were adamant about burning it so we left it with them to burn. Plus I was a bit injured at the time.”

Yes, your injury. Dr. Beckett, why didn’t you institute quarantine protocols when you returned to Atlantis?”

Carson frowned. “I didn’t think it was necessary. We had no idea at the time that the Colonel had been infected with the retrovirus.”

But once you got to the infirmary and found that his wound had disappeared you had to have realized that something had happened.”

Yes, but we didn’t understand what. I took some blood for analysis but Colonel Sheppard seemed perfectly fine so I didn’t see a reason to keep him at that time.”

And when you realized that he was infected with the retrovirus, that it had been transferred to him from Ellia, he was still allowed to wander freely through Atlantis, with no thought about anyone else he might infect?”

I wouldn’t say he wandered freely,” Elizabeth interjected. “He did have a military escort and was later confined to quarters.”

But did any of you even consider that he might be contagious, might be able to pass the retrovirus on to others?” Woolsey continued to press.

Carson and Elizabeth exchanged glances. “No, I’m afraid I didn’t,” Carson admitted.

Woolsey tapped his pen against his notepad and shook his head. “I am seeing some worrying patterns here.” He glanced at the other delegation members but didn’t elaborate. “Now, after that, you decided that Iratus embryos were necessary to create a treatment. Please elaborate on that.”

Carson did so, explaining his thought processes.

But the initial mission to retrieve the eggs ended in failure, with two Marines left for dead?” Ellis questioned rhetorically.

Aye, the Iratus bugs did not like us getting too close to their nest. They attacked, despite our best efforts to hold them off.”

At that point, you returned to Atlantis and informed Dr. Weir of the mission’s failure, as well as the fact that you had no other treatment option available. Dr. Weir, you then decided that it was too dangerous to send another team?” Woolsey asked, writing more notes.

Yes, as you said we had already lost two men. I couldn’t send others into what we knew was a lethal situation for the sake of one man.”

That’s the first sensible decision I’ve heard in this mess,” Ellis muttered.

John resisted the urge to glare at him. He didn’t like how every single decision was being put under a microscope. On the other hand, now that he had his full mental faculties back he could agree that it was the right decision not to risk others for his sake.

And then you decided to inform Colonel Sheppard of this development as well as the fact that you would not be sending another team?” Woolsey prompted, ignoring Ellis’ comment.

Yes, he had the right to know. And I felt he would take the news better from me.”

Yeah, we can see how well that worked,” O’Neill snorted. “Why did you enter alone? There were two armed guards right outside his door. One of them should have entered with you.”

I didn’t see the need for their presence.”

You didn’t see the need? For crying out loud!” O’Neill shook his head. “You knew that the drug they were using to keep Sheppard lucid was losing its effectiveness. Hell, from the reports Sheppard himself had ordered the guard outside his quarters doubled. You had absolutely no business going in there without a guard.”

Elizabeth glared. “I believed that I was in no danger. John Sheppard would not harm me.”

John slouched in his chair because he knew she was wrong, he had attacked her.

Not in his right mind he wouldn’t,” O’Neill agreed. “But he wasn’t in his right mind! How the hell do you think he feels knowing that he attacked you, attacked his men? I can tell you from personal experience that it’s not sunshine and rainbows.” His tone softened. “I know what you were thinking, I’ve been there on both sides but it doesn’t mean it wasn’t a stupid decision.”

John’s head came up at that. O’Neill’s expression showed complete understanding. Huh, maybe he should ask him if he got a chance.

Elizabeth was looking stricken. “I-” She cleared her throat. “I wasn’t thinking.”

O’Neill looked disgusted. “No, you weren’t. Apparently, none of you were thinking during this whole mess. The only one of you who is completely blameless in this mess is Sheppard. He’s the only one of you that didn’t do anything wrong.”

John frowned and opened his mouth.

AHT!” O’Neill forestalled him. “Actions taken while under an alien influence, in this case losing your mind to an alien retrovirus, cannot be held accountable.”

John closed his mouth.

And Rodney opened his. “But I didn’t do anything wrong either,” he pointed out.

O’Neill shot him an exasperated look. “What the hell were you thinking going after him alone? He’d already attacked Weir and the men guarding him. You made the same stupid decision that she did. What did you think would happen?”

Caldwell was trying to kill him! Or the Goa’uld controlling him was,” Rodney defended.

McKay, no one is faulting you for your loyalty to your teammate, least of all me. But it was still a stupid decision to make.”

Rodney slumped in his chair. “The rest of my team had been locked up for disagreeing with Caldwell. I didn’t know who I could trust in the military, they would have been disobeying orders to help me.” He straightened up. “Anyway, Sheppard didn’t attack me!”

No, he didn’t. But you had no way of knowing that he wouldn’t at the time. And because you were down there, you ended up also being exposed to the retrovirus,” Woolsey told him. He looked at the rest of the delegation. “I think we’ve heard enough at this point.”

There is one more thing I would like to clarify first,” Wray spoke up. “Dr. Beckett when you determined that the only one who would have a chance of retrieving the Iratus eggs was Colonel Sheppard, you injected him with a massive dose of the inhibitor. Wasn’t that dangerous?”

Aye, it could have been fatal.”

She frowned. “And you did it anyway?”

I didn’t see that there was much to lose at that point. And I believed that the Colonel would have wanted one last chance at lucidity even if we knew for sure it would kill him.”

John lifted his gaze to meet the doctor’s. “And you would have been right. If I was going to die anyway, I would have preferred going out as myself, at least mentally.”

But the retrovirus wasn’t killing you,” Wray pointed out.

John cocked an eyebrow at her. “It was stripping me of my sense of self, my consciousness, my very humanity. What else would you call it?”

O’Neill nodded at his words, while both Woolsey and Wray looked thoughtful, Chapman looked disgusted and Ellis was blank-faced.

Thank you for your time. If you would excuse us, we need to discuss our findings among ourselves,” Woolsey dismissed them.


Oh, this is horrible,” Rodney moaned as soon as the doors closed behind them.

It wasn’t that bad Rodney,” John tried to reassure him.

Rodney shot him a look. “Are you kidding me? Were you listening in there? They questioned every single decision we made, and it sounds like they found us wanting. This isn’t good.” How could the man not see this? It had to be his hair, he decided. It was screwing up his perception. He glared at it.

I hate to agree with Rodney but I don’t think it looks too good for us either,” Carson said. The doctor looked a bit pale.

Rodney had to admit that Carson had definitely gotten the worst of that interrogation. Then again, the doctor had made some rather questionable decisions during this mess.

I’m sure it will be fine,” Elizabeth said, obviously trying to sound reassuring. But her case wasn’t helped by her worried frown or pale skin.

Oh God, if the delegation made a move against Carson and Elizabeth then what hope could he and John have? “We’re going to be kicked off Atlantis,” Rodney moaned. “Oh God, we’ll be thrown into the deepest hole they can find and forgotten about.”

Rodney!” John grabbed him by the shoulders and gave him a little shake. “That won’t happen. General O’Neill isn’t going to let that happen.”

You can’t know that!”

Everything I know about the man says that he won’t allow that to happen. I trust him.” John’s gaze softened. “So trust me, okay?”

Rodney stared into his eyes. “I- Okay.” He forced himself to relax his tense body.

I’m sure it will be alright,” Elizabeth said again. “I know this type of move. This is them maneuvering for some type of concession. They’ll make their demands and then everything will go back to normal. You’ll see.”

Well, Elizabeth was the expert in diplomatic affairs, he supposed he should trust her judgment. But a nagging voice whispered that it wouldn’t be that simple.

John nudged him with his shoulder. “Come on. They’ll call us when they’re ready for us. Let’s go check in with Ronon and Teyla in the meantime.”

Alright,” Rodney agreed. It was probably a good idea to move away from the conference room. All they would accomplish there would be pacing a hole in the floor. John’s suggestion was definitely the preferred option.

Well, I have a patient I should check in on,” Carson said. He left quickly, tension visible in his hunched shoulders.

You two go ahead. I have some paperwork to review,” Elizabeth told them before heading to her office.

Rodney glanced at John and got a shrug in reply. They quickly left as well.

They found the rest of their team sparring in their preferred gym. The two quickly ended their match when John and Rodney entered.

John, Rodney,” Teyla greeted them. “I take it from your expressions that things did not go as well as hoped for?”

We’re doomed,” Rodney said, collapsing on the bench.

Hey, I thought I told you to trust me,” John glared at him.

I do. It’s the delegation I don’t trust.” He sighed and looked at Ronon and Teyla’s curious expressions. “They picked apart every decision any of us made, and it sounds like they found fault with them all. Hell, they even said the only one blameless in this mess is Sheppard but that didn’t stop the looks of disgust being directed his way or save him from the interrogation.”

John shrugged. “Elizabeth thinks it’s just a tactic to try to get some concessions from us.” He didn’t look too sure of that. “So, either of you feel up for another round?” he asked, changing the subject. “I need to work off some tension.”

Ronon and Teyla exchanged a look before Ronon gestured for her to go ahead while he plopped down next to Rodney.

Rodney watched for a few minutes as the two traded blows with their sticks, then glanced at Ronon thoughtfully. “Can I ask you a question?”

Ronon gave him a look.

Right, okay. I was just wondering. You haven’t seemed to have had an issue with, well, with any of this,” Rodney said as he gestured to himself. “Unlike others, even some of the most open-minded people I know.” He glanced at Teyla briefly, then returned his eyes to the large man beside him. “So I was just wondering. Why?”

Ronon shrugged. “’Cause I understand things happening to you beyond your control, things you didn’t want to happen but now have to live with. Helps that you look nothing like a Wraith.” Ronon grinned suddenly, but it was all teeth, like a shark’s grin. “Plus I figure it makes you stronger and faster, makes it easier for you to take out Wraith. Anything that helps take out Wraith is a good thing.”

John stumbled as he took a hit. He held up a hand to ward Teyla off and turned to face Ronon. “But you’re not going to try to undergo something similar?” he asked suspiciously, proving that he had been listening to their conversation.

Nah. I know neither of you wanted it, and I don’t either. But you might as well make the most of what you’ve gained.”

Huh,” John said, eyeing him for another moment before resuming his spar with Teyla.

Rodney glanced at Ronon also. “Well, thanks for answering.”

No problem,” he grunted, turning his eyes back to the sparring session.

Rodney took that to mean that their little heart to heart was done. He sighed, wishing for a computer. He had been forbidden by John, Elizabeth and Carson from bringing one to the meeting but now he wished he’d stopped to grab one on their way here.

His radio chimed at that moment. “McKay here,” he answered, seeing John reach for his own as well.

Rodney, John, I thought you should know that the delegation is requesting we return to the conference room. Apparently they’ve reached a decision.” Elizabeth sounded worried.

That fast?” Rodney questioned. That couldn’t be good. The only way to have already reached a decision was if they had made it before they even met with them.

I know, the news doesn’t look too promising from this end.”

John frowned down at himself. He had worked up a bit of a sweat. “Er, did they mention how quickly they wanted us there?”


John grimaced. “Alright, we’re on our way.” He ended the transmission and headed over to a small cubicle, pulling a spare uniform shirt out of it. “Would have preferred to shower but this will have to do,” he said as he stripped out of the sweaty shirt and ran a towel quickly over his chest and shoulders before donning the clean shirt.

It was a testament to how worried Rodney was about the imminent meeting that he didn’t get distracted by the sight, however brief, of John without a shirt. “This is not good,” he fretted. “They’re going to make us leave Atlantis, they’re going to lock us up for the rest of our lives. I won’t be allowed to work anymore. I’ll never get a Nobel.”

Rodney!” John grabbed him by the shoulders and gave him a small shake. “It doesn’t look good, I know, but I’m sure it’s not as bad as you’re thinking.”

Rodney stared at him, unable to convey just how wrong he thought John was.

John’s face softened. “It’s gonna be okay. Whatever happens, we’ll face it together, alright?”

Rodney nodded, swallowing back the rest of his fear.

We shall accompany you,” Teyla said as she and Ronon moved to follow them to the door. “Even if we cannot join you in your meeting, we shall wait outside as moral support.”

Ronon shrugged. “If they try to make you leave I can always shoot them and throw them through the gate,” he offered.

Rodney actually found himself considering taking him up on the offer.

Thanks, buddy,” John said, briefly patting his shoulder. “But I’m sure it won’t come to that.” He turned and gave Rodney’s shoulder another squeeze. “Alright, let’s go see what they’ve decided.” He led them out the door and to the transporter.

As the doors closed behind them, Rodney found himself praying to a God he didn’t believe in that things would work out in their favor.

Chapter Text

Elizabeth was waiting for them outside the conference room doors. She gave them a nod as they reached her. “Okay, Carson should be here any minute,” she said.

I’m here,” Carson called as he approached.

Good.” She took a deep breath.

Any idea what their decision is?” John asked her when she made to open the door.

No.” She shook her head, looking worried.

But it doesn’t look too good, does it?”

No, it doesn’t.”

Teyla stepped forward. “I would speak with them if you thought it might do some good,” she offered.

Thank you Teyla, I appreciate it. But I’m not sure how much value they would put on your opinion,” Elizabeth replied. “Okay, we really shouldn’t keep them waiting any longer.” She reached out and keyed the doors open.

John glanced at Rodney, trying to offer him some wordless reassurance as they followed her in.

Elizabeth stopped in front of the conference table and stood there, John, Rodney and Carson coming to a stop slightly behind her. “I take it you’ve reached a decision,” she said, not beating around the bush.

In part,” Woolsey said before gesturing to the table. “Please be seated.”

Rather than taking her previous seat, Elizabeth sat in one of the chairs directly in front of the delegation. John took the seat to her right with Rodney next to him, while Carson sat on Elizabeth’s left.

Woolsey looked nonplussed for a moment before clearing his throat and glancing at his notes. “This incident has simply highlighted a need for more oversight on this expedition. The leadership here has shown a pattern of questionable ethics in their decision making. In particular, we are extremely concerned with Dr. Beckett.”

A look of shock passed over Carson’s face. “Me?”

Yes. While the reports show that every single one of you has made questionable decisions, you, Dr. Beckett, have shown a worrying pattern of disregard for protocols and ethics when they get in your way.”

I know that I made a mistake in bringing the retrovirus with me but-”

Woolsey held up a hand and interrupted him. “I am not speaking of just this incident with the retrovirus. I am speaking of a pattern of conduct that goes back to the beginning of the expedition. Your experimental ATA gene therapy, while a success, did not follow proper testing guidelines. What are the long term consequences to those who have received it? This is something that would have been studied in controlled, long term testing before it would have been approved for wider use.”

John felt Rodney shift beside him at the mention of the gene therapy and laid a hand on his arm to settle him down.

Well, um, look it was impossible to get FDA approval for the gene therapy due to the classified nature of the program. I took every precaution that I could but the fact is that we needed more people with the ATA gene. And I’ve been very diligent in getting samples and performing check-ups on everyone who went through the therapy,” Carson defended himself.

And I signed off on the gene therapy because we needed more personnel who could use the technology,” Elizabeth added, showing her support.

Yes, and we don’t disagree with the need for the therapy. It is simply the first in a pattern of questionable ethical decisions. Then we have your work on the Hoff drug.”

I didnae tell them to use it on the entire population, I advocated for more testing,” Carson interrupted.

Yes but, again, it is part of the pattern. As is the use of a prisoner, the captured Wraith, in the testing. That is a violation of so many protocols dealing with POWs that I wouldn’t know where to begin. Add in the fact that the Wraith died as a result,” Woolsey trailed off shaking his head.

John shifted uncomfortably. He had agreed to, even argued Elizabeth into, the decision to test the drug on ‘Steve’.

Elizabeth leaned forward. “What is the point of this? These decisions were already debated when we returned to Earth for our debriefing.”

The point, Dr. Weir, is that there is a pattern of questionable ethics.” Woolsey turned to Carson. “You are the Chief Medical Officer. But reading your file I see that you had been mainly a researcher for the last five years. Before the expedition when was the last time you actually practiced medicine instead of research?”

Carson shifted. “It had been a while.”

And yet you were made the CMO.”

We needed people who could fill multiple roles,” Elizabeth interjected.

Yes, back when the expedition was heading into the unknown with no certain way of reestablishing contact with Earth, that was the case. But now you and Earth are in regular contact, with new personnel arriving with each journey of the Daedalus. Therefore, it is the decision of this delegation that there needs to be a change in the roles of certain personnel.” Woolsey looked straight at a nervous Carson. “Dr. Beckett, we thank you for your work to date as the CMO. From all reports you have treated your patients well and to the best of your abilities. Your medical research has also, for the most part, been good work, if lacking in ethics at times. So it is the decision of this delegation that you may remain here and work on medical research but that you are no longer the CMO. Instead, that role shall pass to a practicing doctor with strong ethics and moral fiber. All medical research will be approved or denied by the new CMO, who will work with the CSO to determine the feasibility of each project. With the new CMO’s permission, you will still be allowed to treat patients but any experimental therapies must be approved by the CMO and CSO. Also, while we are not requiring it at this time, we strongly suggest that you take a refresher course in ethics in regards to research.”

John watched as Carson slumped at the news. But it could have been worse; at least he would be staying on Atlantis. As much as John wanted to be angry on his friend’s behalf, he had to admit that the delegation had a point. Hell, even John had thought that Carson had made some big mistakes recently, and now he was being called on them.

Carson merely nodded in acceptance.

Elizabeth was frowning. “I have full confidence in Carson Beckett. He has made some mistakes but he is a talented doctor and brilliant researcher.”

Which is why he’s being allowed to remain and work here,” Woolsey told her.

As the leader of this expedition it is my choice who the CMO is and I stand by my choice of Carson Beckett.”

O’Neill shook his head. “He’s made too many mistakes. He can stay but he needs to report to someone else.”

And who will this new CMO be?” Elizabeth asked angrily.

Woolsey and O’Neill exchanged a glance. “It isn’t final as we hadn’t made our decision regarding Dr. Beckett until we interviewed you earlier,” Woolsey began. “But, if she agrees, our choice is Dr. Allison Brightman.”

Carson nodded his head at the name. “I’ve met her, she’s a good doctor and she has a good sense of ethics. If she agrees I think she would do well here,” he told Elizabeth, obviously having accepted the delegation’s decision.

Carson, we can fight this,” Elizabeth told him.

No, Elizabeth, I accept that there are consequences for my actions. I agree, it is probably best that I have someone check over my work.” Carson sounded resigned to his fate.

Dr. Weir, I would be more concerned with your own position if I were you,” Woolsey told her.

She blinked at him in shock. “My position?”

John stiffened. Oh hell, first Carson was demoted, now Elizabeth was being threatened. If they were being forced out, then what hope did he and Rodney have? Even if her support of him hadn’t been for his own sake, she had still been one of his main proponents. And if that support was gone then his and Rodney’s current situation became even more precarious.

It was under your leadership that these decisions were made. You even authorized most, if not all, of them.”

I made the best choices I could based on the advice of my people,” Elizabeth countered. “I am not a medical doctor or a member of the hard sciences, I can only act based on the information that I receive from them.”

Yes, but you appear to be too close to ‘your’ people, often allowing sentiment to influence your decisions. Case in point, your choice to visit Colonel Sheppard without an armed escort. Looking over the reports, there appear to be multiple times that you allowed your feelings to interfere with your decisions. There have also been some concerns raised that you are out of your depth in your current circumstances.”

Excuse me?” Elizabeth narrowed her eyes.

Dr. Weir, you are a fine diplomat. But do you really think diplomacy will resolve the situation with the Wraith? How do you plan to negotiate with a species that sees us as food?”


Woolsey continued before she could say anything more. “And we have heard of the incident where a group of Wraith managed to incapacitate most of the personnel here. An incident that had come about because you trusted intel from a people that had already betrayed you once before.”

Elizabeth was very tense. “We have no proof that the Manarians knew the information was a trap.”

But did you even consider it?” Woolsey questioned before turning to face John. “Colonel Sheppard, were you aware of where this intel had come from?”

John glanced briefly at Elizabeth. “Not until the debriefing after the attack.”

And if you had known?”

John swallowed. He really hated to be put in this position. He wanted to support Elizabeth but at the same time doing so would be undermining his own position. This time he didn’t look at Elizabeth, hoping she would forgive him. “I would have found it suspect and would have urged greater caution. It’s no secret that I don’t trust the Manarians and would be very suspicious of any ‘intel’ that they provided.”

Woolsey nodded. “Dr. Weir, why didn’t you consult with Colonel Sheppard about the origin of this intel?”

I hadn’t thought it was relevant. The Manarian’s had apologized for their part in the Genii’s attack and had been a valued trading partner. Again, there is no proof that there was any duplicitousness on their part.”

But they had betrayed you in the past,” Woolsey pointed out again. “From a security standpoint, the military should have been more involved in verifying the intel. Which is why there are concerns that you don’t have the necessary knowledge to interpret what should fall under the military’s purview. It has been pointed out that it might be better for someone with military experience to take command.”

John glanced at the other members of the delegation as Woolsey spoke. O’Neill looked like he wanted to interject but was keeping silent, Wray was neutral but Chapman and Ellis’ usual air of disgust seemed more anticipatory than it had been. Things were not looking too hopeful for any of them. He glanced at Elizabeth, her body tense and radiating controlled fury.

However,” Woolsey continued before Elizabeth could interrupt, “for the most part things have worked out in the end. It has also been pointed out that things didn’t turn out well the last time a military officer tried to take command of this city. For those reasons, we are allowing you to keep your post.”

Elizabeth breathed a sigh of relief, the tension beginning to ease from her frame.

But, you will be under greater scrutiny going forward. An agent of the IOA will periodically come to audit this base to ensure that procedures are being followed and if any misconduct is found you will be replaced.”

I understand,” Elizabeth told them.

Good. Now we come to the more difficult part of our decision.” Woolsey turned to look at John and Rodney. “Though little to no fault lies with you, nevertheless the two of you have been irrevocably altered.” He gave John and Rodney an apologetic look. “I am afraid that we just don’t know what to do with you two. It goes without saying that you can’t return to Earth to live, not openly, the risk is just too great. And for obvious reasons, it isn’t feasible for you to remain here.”

Why can’t we remain here?” Rodney asked. “We’re still the same people, we can still do our jobs.”

Woolsey blinked at him, nonplussed. “I’m not sure how you can say that Dr. McKay. I mean-” He gestured at them, unsure how to continue.

Rodney rolled his eyes. “Okay, so we’re not the same physically but we’re still the same mentally. Ask Carson or any of the other medical doctors, all our tests show that our brain scans are the same as before we were infected with the retrovirus.”

Woolsey cleared his throat. “That may be true but how can we justify making others uncomfortable by asking them to work with you now?”

Rodney frowned. “What do you mean? I haven’t had any problems. Okay, there was some discomfort the first couple of days but once people got used to the new sight everything went back to normal.” He turned to John. “Have you had any issues? I mean, I know soldiers aren’t as intelligent as-”

No, no problems on my end,” John cut him off before he could finish what was sure to be an insult to the military portion of the expedition.

Colonel Ellis leaned forward suddenly, pinning Elizabeth with an intense look. “Do you mean to tell me that these two have had unrestricted access to this base?”

Of course not,” Elizabeth denied. “They were restricted from high access areas such as the control room, the jumper bay, the armory and the ZPM power chamber, only being allowed access to those areas with an escort. And Dr. McKay was only allowed to work in the lab when supervised by Dr. Zelenka. But I didn’t see the need to keep them confined to their quarters. As stated, all medical reports showed that they were still themselves so I did not see a need to continue to punish them for something that you yourselves have stated was not their fault.”

And they never violated those restrictions?” Ellis asked, something dark in his tone.

Elizabeth winced. “The one time they did there were extenuating circumstances. I sent you the reports, we had an incursion from the Wraith and without Colonel Sheppard and Dr. McKay’s intervention the city would likely have fallen to the Wraith.”

Yes, I read the reports and they disturbed me greatly.” Ellis glared at her. “The very fact that the Wraith were able to gain access to this base; were able to knock out most of the population.” He shook his head in disgust. “And then these two not only violated their orders and entered restricted areas, but they also hacked the computer system to do it.” He turned to the rest of the delegation. “You can’t seriously consider them anything but a security threat.”

Woolsey looked torn. “I agree that normally it would be a serious violation but, as Dr Weir has said, there were extenuating circumstances and their actions proved vital to saving the lives of everyone on Atlantis.”

Exactly!” O’Neill agreed. “Sometimes you have to disobey the rules in order to save the day. It’s not like they did it any other time, right?” he asked, eyeing them across the table.

No!” Rodney and John voice simultaneously.

Ellis looked disgusted. “We have only their word for that. With how easily McKay was able to hack the system it’s not like they couldn’t cover their own tracks. How do we know that they weren’t the ones to signal the Wraith to attack? Don’t they share DNA with them now? How can we trust where their loyalties lie?”

John bristled, his claws scratching the surface of the table as he leaned forward. “And what would be the point of that? We took out the Wraith,” he reminded them.

You could have planned it to lure us into trusting you, to convey a false sense of security,” Chapman countered.

For what end?” Elizabeth asked. “There would have been no better time for the Wraith to gain control than at that point, with most of the expedition stunned and helpless. There would be no need to instill a false sense of security.”

Yes, I agree, that would make no sense,” Woolsey said, getting nods of agreement from O’Neill and Wray while Ellis and Chapman both looked disgruntled at losing the argument. He turned to Elizabeth. “So there have been no issues, no complaints about Colonel Sheppard or Dr. McKay?”

She shook her head. “None. At least none relating to their new appearance.” She shot Rodney an exasperated look. “Just the normal ones about Dr. McKay’s tongue lashings.”

Rodney folded his arms over his chest and huffed in annoyance. “Well then maybe they should spend less time complaining and more time focusing on their jobs instead of doing sloppy substandard work.”

Hmm.” Woolsey looked thoughtful. “We’d have to discuss it of course, but it might be possible for Dr. McKay to remain and continue to work. Of course, it would be up to the new military commander whether Colonel Sheppard would be able to remain.”

John felt his hope plummet. This was it, confirmation that he was losing his command. He’d suspected it but now that it was happening he realized he’d been holding out hope for a last minute rescue.

Elizabeth frowned. “If it’s possible for Dr. McKay to stay and continue his duties why can’t Colonel Sheppard also continue as the military commander?”

Ellis shot her an incredulous look. “Look at him! He’s blue for God’s sake! Do you really think any of the men are going to want to follow his orders when he doesn’t even look human any longer?”

Elizabeth glared at him. “Why don’t you ask them?”

O’Neill was also glaring at Ellis. “I agree, the only way to get an answer to that is to ask the men.”

Wray looked thoughtful. “I would like a better picture of the circumstances as they stand here, more viewpoints would be welcome.”

Woolsey was nodding. “A very good point. We should get an idea of the general opinion of the population before making a decision.”

Again Chapman and Ellis were the only dissenters.

I do not see how that would be helpful,” Chapman said. “Their friends would say anything to keep them here, while others could be intimidated to lie.”

You can’t seriously be considering this? McKay is one thing but Sheppard has a track record of disobeying orders,” Ellis argued. “Hell, he’s in violation of the regs, involved in conduct unbecoming!”

The room went silent with that accusation. John froze, feeling Rodney’s stricken gaze. How did Ellis know? While he’d told Rodney that he didn’t care what the delegation said about their relationship, he hadn’t really expected it to be brought up in this manner. His eyes slid to O’Neill but the way the General was glaring at Ellis made it  clear that he wasn’t behind the outing.

I hope you have proof of your claims,” O’Neill started, glaring at Ellis. “Because it sounds to me like you’re just throwing accusations out there because you’re not getting your way.”

An interested party came to me last night with claims that Sheppard and McKay are involved in a homosexual relationship, with Sheppard spending the night in McKay’s quarters almost every night. I checked, and that’s where he was last night.” Ellis glared at John.

Who is your source?” Elizabeth asked. John glanced at her and noticed that she looked a bit shocked but was rapidly pulling herself together. A glance at Carson showed no surprise, only anger directed at Ellis.

I don’t feel comfortable revealing that information at this time,” Ellis responded. “I don’t want him being coerced into withdrawing the claim.”

Why didn’t you say anything before this?” Woolsey asked.

I didn’t see the point. I didn’t think any of you would actually consider letting them stay here,” Ellis defended. “I figured he was going to be tossed out of the military anyway so there wasn’t a need to air all of his dirty laundry. But even if you think the military portion of this base would put up with a blue-scaled freak as their commander, they wouldn’t accept one that’s a faggot!”

Wray suddenly glared at Ellis. “Do you have a problem with homosexuals?”

They shouldn’t be allowed to serve in the military. But if they do they’re supposed to keep it in their pants, not dishonor the uniform!”

We’re getting away from the topic at hand.” Woolsey sighed before turning to the senior staff. “Colonel, Doctors would you mind stepping outside, please? I would like to hear the information behind Colonel Ellis’ accusation and he won’t share that with you present. Please don’t go far, this shouldn’t take long.”

John stood woodenly and headed for the door, Rodney right on his heels with Elizabeth and Carson following. He ignored the concerned looks from Teyla and Ronon who still waited nearby, leaving Elizabeth to quietly explain the current situation.

Once the doors closed behind them Rodney immediately began to talk, his hands arcing through the air. “Oh, I knew I shouldn't have let you talk me into this. We had a good chance of keeping Atlantis and now it’s gone. All because of your military’s backwards view of homosexuality.”

You don’t have to lose Atlantis,” John told him, his heart breaking as he spoke. “I’m the one who broke regulations, you’re a civilian, they don’t apply to you.”

Oh please, if you go, I go.” Rodney waved a hand negligently, as if there was any doubt of his answer.

Elation filled John at the casual reassurance. “Then I don’t care if we lose Atlantis, I meant what I said when I told you that you’re more important.” He calmly met Rodney’s wide blue gaze, letting him see the sincerity there. “Besides, Ellis was going to find some reason to get rid of me, if not this then something else. He wants the city for himself.”

Well he’s not going to get it,” Elizabeth said firmly, a determined look upon her face. “If he succeeds in removing you I will fight his appointment with everything I can. It will be a Pyrrhic victory for him,” she vowed. “And he’s made a big mistake already with his attitude. You see, I’ve met Camile Wray before. And I know that she’s been with her partner, a lovely woman named Sharon, for several years. So Ellis has made himself an enemy and us an ally with his thoughtless comments.” She had a smug air about her as she spoke. John was glad to see that she didn’t seem to hold any hard feelings for his not backing her up in there. She gave him a glance then nodded, confirming that fact.

Carson stepped forward and clasped both of their shoulders. “Now don’t go planning your goodbyes yet lads. I might be able to salvage this yet.”

John frowned at him. “What are you talking about Carson?”

Never you mind. I got you into this mess with my retrovirus, I’m going to do my best to get you out of it. Just don’t argue when I make my case in there,” he told them just as the doors opened to readmit them.

They reentered and took their seats.

Well, Colonel Ellis’ information does seem legitimate. Do you deny the allegations Colonel Sheppard?”

John took a deep breath. “No.” Even if there was no proof he would not deny Rodney.

O’Neill looked briefly uncomfortable at his admission.

Then I don’t see how you can retain your post. Even if you weren’t changed, once this information came to light you would have been removed from your post pending a court-martial and discharge and thus unable to serve as military commander of this outpost,” Woolsey pointed out.

Excuse me, but if I can interject I have some information that is germane to this topic,” Carson said once Woolsey had finished. “I just didn’t see the need to mention it earlier as it is private and personal but if you’re going to use this as an excuse to toss them out then I think you need to hear it.”

John frowned at him, wondering again just what he was planning. “Carson-” he started to say, only to stop at the glare he received from the doctor and the jab to the side from Rodney.

I’m not sure what information you believe would mitigate the situation, but by all means, proceed.”

Thank you,” Carson said before clearing his throat. “Now, I’ve told you that mentally the Colonel and Rodney are the same as they were before the change, however, there is one area where that is not quite accurate. You see, with their changed bodies, the chemical makeup of the pheromones they produce has also been changed as has their body chemistry. What once might have attracted them no longer does, and vice versa.”

Are you trying to say that the change made them gay?” O’Neill asked incredulously.

No, I’m saying that the change in their body chemistry made them each attracted to the only other person with a similar body chemistry. I’m sure that if you investigated that you would find that there was no such relationship prior to them being infected with and changed by the retrovirus.”

John bit his tongue to keep from blurting out that Carson was wrong, he had been attracted to Rodney, cared for him before this. But that would spoil what Carson was trying to do.

Woolsey frowned. “So you are saying that their changed body chemistry attracts them to one another but that doesn’t excuse Colonel Sheppard for violating the regulations he swore to follow.”

Carson frowned at him. “Would you really begrudge them a bit of comfort after what they’ve been through? Do you really think anyone else would want to be with them now?” He gave them an apologetic look as he spoke, then continued. “And there is the fact that certain bits were physically changed and might not fit anymore.” A blush suffused his cheeks at the last.

Woolsey coughed. “Yes, well. I see.”

O’Neill rolled his eyes at Woolsey’s stammering. “Sheppard,” he said. “Is what the Doc says true? There was no you and McKay prior to this?” He gestured at them.

John straightened up as Rodney poked him again. “Yes, sir. This all happened after the change.” Not a lie since they hadn’t gotten together until after their mutation. There was no need to mention that there had been unspoken emotions prior.

O’Neill nodded. “Well, there is a clause in the SGC’s guidelines that a person can’t be held accountable for actions taken due to being altered by an alien influence. I don’t think it gets more altered than this.” He shot a quick glare at Carson. “Provided, of course, that you have proof of your claims.”

Oh, aye. I can get you the reports immediately.” Carson nodded.

John shot him a glance, wondering just how long he’d planned this to have it already documented.

Then, pending review of these reports, I don’t see how we can rightly charge Sheppard with Conduct Unbecoming.” O’Neill gave John a look. “McKay? Really? You have my condolences.”

John bristled but held his tongue, not willing to upset the renewed hopes of keeping his position. And a hand on Rodney’s arm kept Rodney quiet as well.

Well, in light of this new information, I think we should see about getting some interviews set up,” Woolsey said.

Provided each person agrees, we would like to be present for the interviews,” Elizabeth responded, gesturing to herself and the three men.

So you can intimidate them?” Chapman sneered.

If they don’t feel comfortable speaking in our presence then we will, of course, wait outside. I would just like to hear the questions asked along with their answers and I’m sure Colonel Sheppard and Dr. McKay feel the same. After all, it is their fates on the line.”

Woolsey thought about it for a moment. “Agreed, but only with their permission.”

Ellis simply looked constipated.

Elizabeth gave the delegation a polite smile. “Of course. Now if you could tell me who you would like to start with I can arrange to have them paged here, providing it doesn’t interfere with their current duties.”

Of course,” Woolsey agreed with a nod. “Well, we might as well start with those higher up in the chain of command who are more likely to interact with Colonel Sheppard and Dr. McKay on a daily basis. Let’s start with Major Lorne. I’m sure he can provide some insight into how the military portion of this outpost feel about Lt. Colonel Sheppard and his change.”

Of course,” Elizabeth agreed. “And I’m sure you’ll also want to interview Teyla Emmagan and Ronon Dex, to get a native Pegasan’s viewpoint,” she suggested.

Woolsey nodded. “Yes, but first let’s hear from those from Earth. Please contact Major Lorne.”

Chapter Text

Rodney sat at the conference table, listening as the delegation from Earth interviewed various members of the expedition. Most members of the expedition had agreed to allow the senior staff members to remain for the interviews, and Rodney found himself surprised and unsure how to react to their answers to the delegation’s questions.

It had started with Major Lorne, as he was the first one to be interviewed.

Thank you for joining us, Major Lorne,” Woolsey greeted him. “We are trying to come up with a solution to the dilemma of what to do with Colonel Sheppard and Dr. McKay, and would like to hear from various members of the expedition.”

Lorne sat up straighter at that and glanced toward Rodney and John.

Woolsey noticed his gaze. “We want you to be comfortable enough to answer all our questions honestly. If you want, we can have the room emptied of everyone but ourselves,” he offered.

Lorne shook his head. “No sir, that’s not necessary. There is nothing I have to say that they can’t hear.”

Very well.” Woolsey shuffled some papers, clearly just to have something to do with his hands. “Both Colonel Sheppard and Dr. McKay feel that they are still capable of performing their duties and Doctors Weir and Beckett agree. What is your opinion of that?”

If they think they can carry out their duties then I don’t see any problem.”

Woolsey blinked at him. “As the 2IC of the military here on Atlantis, it has been up to you to fill in for the Colonel since he was infected with the retrovirus. As such, you would have a better idea of the reaction of the other military members. Are you saying that you don’t see a problem with them continuing to work under Colonel Sheppard?”

No sir, I don’t.”

Oh for God’s sake, look at him! He’s blue! You can’t seriously tell me that you won’t have an issue following his orders?!” Ellis burst out.

Lorne raised an eyebrow at him. “I’m surprised that you would think that the color of a man’s skin means we shouldn’t obey his orders. Sir,” he added after a brief moment.

Ellis flushed angrily at the pointed remark about his own skin color. “That’s not the same thing!”

I don’t see why not?”

I’m human!”

And despite their physical appearance so are Colonel Sheppard and Dr. McKay.”

Rodney could only watch in awe as Lorne, seemingly unintentionally, worked Ellis up into a state of rage but he could see what was coming next and he mentally braced himself for it.

He’s fucking McKay! Are you saying that none of the military members will have a problem taking orders from a fucking faggot?!”



Warning reprimands came from both Woolsey and O’Neill while Wray merely glared at Ellis who fell silent and sat back with an irritated huff.

Woolsey cleared his throat. “Despite his crass language, Colonel Ellis does have a point. You might not be aware but it has been proven that Colonel Sheppard and Dr. McKay are involved in an intimate relationship.”

No sir, I wasn’t officially aware.”

Officially?” Woolsey asked.

The policy is Don’t Ask, Don’t Tell, Don’t Pursue,” Lorne reminded him. “If there were hints of a relationship I couldn’t ask and the Colonel couldn’t tell. I chose to follow policy and not pursue the matter.”

Yes, well,” Woolsey stammered, not having expected that answer.

Oh, for crying out loud,” O’Neill muttered. “Well, Major, now that you know, officially, will there be any problems?”

Not on my end, and not with most of the military members. To get this posting you have to be pretty open-minded. You get too much weird stuff thrown at you not to be.”

You said most,” Chapman pointed out, latching onto that part of Lorne’s statement. “That means you think there will be problems with some of the men.”

Well like I said, you have to be pretty open-minded to last in a post like this. Despite the SGC’s best efforts at screening, some individuals manage to slip through the cracks. They usually end up requesting re-assignment before too long. Those are the ones who might have a problem with Colonel Sheppard retaining command.” He leaned forward to stare at each member of the delegation. “But I can say this with confidence: If you ask them, the majority of the men and women of this command will state that they couldn’t be prouder to serve under Colonel John Sheppard, regardless of his skin color or sexual orientation.”

And Dr. McKay?”

Well I can’t speak for the scientists, I don’t know most of them well enough, but I doubt there is a man or woman among the military who have a problem with the doc staying.”

Rodney couldn’t have been more surprised by his words and it must have shown on his face.

Lorne looked at him steadily. “Come on Doc, you must have noticed that everyone’s attitude changed after the Wraith attack. You risked your life to defend those who couldn’t defend themselves. Before that, all we had to go on was the constant complaining you did. Now we can see that, for all your complaining, when the chips are down you come through for us, usually with a technological solution but sometimes in other ways. You’ve earned our respect and loyalty.”

Rodney didn’t know what to say. He opened and shut his mouth a few times until John laid a hand on his arm and squeezed.

Wow, a silent McKay. If one of your skills is silencing loud-mouthed scientists I might have to steal you to work for me,” O’Neill commented.

Sorry sir, probably a one-time occurrence.”

Drat,” O’Neill mock complained.

Ahem. I believe we are getting off topic,” Woolsey said to reclaim their attention. He turned back to Lorne. “So in your opinion, the only members of the military who would take issue with Colonel Sheppard’s command are the ones who would not have lasted out here anyway?” At Lorne’s affirmative response he asked, “What about any new personnel who are transferred in, those who would not have known the Colonel before this incident? How do you think they would react?”

I couldn’t say for sure. It would probably be an adjustment for them but not one that they couldn’t handle. Just coming out here is a big adjustment, so if they can handle the posting I don’t see why they couldn’t handle the Colonel’s appearance.”

Hmm.” Woolsey made a note on his pad of paper. “Thank you for your time Major, your answers have been most enlightening.”

Sir,” Lorne nodded to him and the rest of the delegation as he stood. He stopped and turned to O’Neill, snapping off a salute that the General returned after a brief moment. Then he turned and offered a second salute, this time to John, clearly showing where his loyalties lay.

Rodney could tell how touched John was by the display, and this time it was his turn to place a hand on John’s arm to offer support.

After Lorne left, Woolsey again shuffled his papers. “Let’s call Dr. Zelenka next.”

And so it went. Rodney had been there through almost every interview and he still couldn’t quite believe the support that they had received from the members of the expedition. While he wasn’t surprised to hear them support John, it was their support of him that blew his mind. While there had been a few who requested the senior staff leave the room for their interviews, it was a very small minority that consisted of those that Rodney hadn’t foreseen lasting long in Pegasus, like that chemist, Wilson, Winslow, Wilkins, whatever his name was.

But most had been so supportive of the two of them.

Whether it was Cadman telling off Woolsey for presuming any of them had been hired for their looks, Katie Brown professing her happiness that he and John had found each other or Radek complaining that the only thing he couldn’t put up with was the long hours Rodney expected - whatever it was, Rodney was touched beyond words. He had known that the expedition was made up of intelligent people, even if they sometimes didn’t show it or seemed to be lacking in common sense, but to hear all of the support for him and John, never mind what the bigoted laws said, was heartwarming. His favorite moment had to be when Stackhouse finally lost his patience with the delegation.

Look, I don’t know how many times you are going to ask me the same question but my answer isn’t going to change. I don’t care what Colonel Sheppard and Dr. McKay look like. I don’t care if they screw like rabbits, as long as I don’t have to see it. All I care about is that they can do their jobs, which they have proven that they can. They saved my life, the lives of my team, and probably the lives of everyone in this city. They deserve our respect and our gratitude, not this farce.” He leaned forward. “Hell, we should be thinking about the benefits the changes gave them. If they hadn’t been changed the city would likely have been lost when the Wraith attacked. Their changes have made them immune to Wraith stunners and given them a physical edge against them. Instead of sitting here and questioning us over and over, you should be thinking of ways to use this to our advantage against the Wraith.”

Thank you, Sergeant,” O’Neill told him, looking like he wanted to cheer him on, while the rest of the delegation was looking discomforted - or downright irritated in the case of Chapman and Ellis - by his speech.

Eventually, after three wasted days that Rodney would never get back, they had interviewed every member of the expedition. Well, not completely wasted. He now knew how the other members of the expedition felt about him, explaining the looks he had been receiving lately.

The only people left to hear from were not technically expedition members. Rodney knew that Teyla and Ronon would be supportive but he was pretty sure that the delegation wouldn’t put much stock in their opinions. At least they were allowing them both in at the same time. He dreaded what Ronon’s interview would be like without Teyla’s calming presence.

Ms. Emmagan, Mr. Dex, thank you for joining us,” Woolsey greeted them as he had greeted everyone else which was more than Rodney had expected.

Teyla inclined her head to him. “Thank you for agreeing to hear us out. Colonel Sheppard and Dr. McKay are good friends but more than that they are good men and I believe they are our best chance of dealing with the threat of the Wraith, permanently.”

Wray tilted her head in confusion. “Funny you should say that since it was Colonel Sheppard who woke the Wraith in the first place.”

He may have woken them early but they would have eventually awoken on their own. The Colonel’s affinity for using the Ancestors technology and Dr. McKay’s brilliance when it comes to technology are invaluable in the fight against the Wraith. They are necessary here.”

There are others who can use the technology, other scientists. What makes these two so special?”

Ronon leaned forward. “My world was technologically advanced, more advanced than yours in some ways,” he said. “And we still were wiped out by the Wraith. A large part of that was because of a cowardly traitor who threw away countless lives to save his own hide. You want to fight the Wraith and succeed? You need someone who will inspire loyalty, who won’t waste his men’s lives. Sheppard’s that man. As for McKay?” He shrugged. “He talks and complains too much but I’ve never seen anyone more skilled when it comes to tech solutions.”

Obviously they have inspired a lot of loyalty as shown by the support they have received from the members of this expedition and that speaks well for their character. But we aren’t here to judge their character, we are here to judge their fitness to perform their duties.” Woolsey clasped his hands together on the table. “As natives of this galaxy, how do you think others will react upon meeting them? I understand that you yourself had a difficult time adjusting to their change in appearance Ms. Emmagan. So, knowing that, wouldn’t they be a risk to forming any beneficial relationships with other worlds?”

I did have a difficult time adjusting,” Teyla acknowledged. “And yes, I can see others reacting poorly upon a first meeting. I admit that I do not see how they could continue to go through the Ring as part of a first contact team,” she said with an apologetic look in Rodney and John’s direction. “But that does not mean they can not perform their other duties.”

The thought of no longer being on a team wasn’t necessarily a bad thing in Rodney’s opinion. It would mean that he could spend more time in the lab. Granted, he liked being a part of the team, he actually had friends for once. But he could do without all of the life threatening situations they found themselves in on missions. He wasn’t sure John would be quite as accepting though.  A quick glance at John confirmed that the idea wasn’t sitting well with him. His unhappiness had a resigned quality to it though, as if he knew that Teyla was right.

John liked going on missions through the Gate. He wouldn’t like being grounded in the City. Actually, he might start to wonder what kind of military commander he could be if he never left the city. How was he going to inspire the troops like Ronon said if he was stuck in Atlantis full time?

Rodney could practically see these thoughts running through John’s head and he resolved to do everything he could to derail them. There was still plenty of work for John to do and Rodney would make him see that. It looked like it would be his turn to offer comfort and reassurance this time. After Carson’s ridiculous pheromone theory, John had pulled him aside and tried to reassure him that Carson was wrong. Rodney knew how much John hated talking about his feelings and yet that seemed to be all they did lately, not that he was much good at it. Hopefully, he would be able to reassure John in turn that he still had a place here, a job to do. And if he started feeling caged in he could always take a jumper out.

Rodney quickly put those thoughts aside for later as Woolsey shuffled his papers in preparation of speaking.

Well, thank you for your time. You have given us much to think about.” He turned to the senior staff members. “Colonel, Doctors, if you would please excuse us we have much to discuss.”

At the clear dismissal, everyone except the members of the delegation stood and headed for the door. Rodney tried to get a sense of what each was thinking but reading people was not his forte and all he could determine was that Ellis and Chapman were both irritated and disgusted which had basically been their mood since they arrived.

They filed out and were met with the curious gazes of those working in the Gate Room.

They need time to discuss what they have heard and come to a decision,” Elizabeth informed them. They quickly went back to work.

Any idea how they might be leaning?” John asked. Rodney could tell he was nervous only because he felt the same way.

Only Chapman and Ellis,” Elizabeth answered. “And they clearly had their minds made up from the beginning. No,” she shook her head. “The others are playing things too close to the chest for me to get an accurate reading but I think General O’Neill is on our side.”

It’s not too late to shoot them and toss them through the Gate,” Ronon offered, again.

Don’t tempt me,” Elizabeth muttered before anyone else could respond in the negative, again.

Elizabeth!” John uttered in shock.

Rodney was feeling some of that shock himself and found himself staring dumbfounded at the normally diplomatic and tactful expedition leader. Then again, after they had threatened to remove her and replace her with some military idiot he could see where she was coming from.

I’m sick of having all of my decisions questioned and putting up with certain bigoted and small minded individuals. It’s been a long few days, for all of us, and I just don’t want to have to deal with them any longer.” She sighed. “Sorry.”

Teyla gently touched her arm. “It has been a very stressful time, for all of you. Come, I will make you some tea so you can relax.” She turned her gaze on the rest of them. “It would do you all some good to find something relaxing to do while you wait. It does you no good to get worked up while waiting for a decision, good or ill.” She led Elizabeth from the room.

Rodney was just beginning to contemplate heading to the lab, work would relax him, when his gaze landed on John and he began to reconsider. Maybe it wasn’t a good idea to leave John on his own right now. He could be a good boyfriend. “Want to watch a movie, or maybe play a round of computer golf?”

John eyed him for a moment before rolling his eyes. “I’m fine Rodney, go ahead and go to the lab, I know you want to.”

What? No, no, I want to spend time with you,” he protested.

We spend plenty of time together, we don’t have to be inseparable every minute. Besides, I think I’m going to go for a run.”

I could join you,” Rodney offered, kicking himself as soon as the words left his mouth. Why had he said that?

Now John was giving him an incredulous look. “You hate running, you hate any kind of exercise. That’s not going to relax you.” He blew out a breath. “Look, I know that you’re worried about how I’m taking all of this and I appreciate that but I’m fine. Now, as much as I’d hate to turn down an offer from you to voluntarily join me for a run, I know that isn’t what you really want to be doing. So go ahead and go to the lab. Yell at some of your minions, solve some mystery of Ancient technology. Just do something that you’ll find relaxing, okay?” He grinned at him. “I’ll take you up on that offer for a run some other time.”

Oh no,” Rodney said, waving his arms in protest. “That was a one time offer and you turned it down. Good luck getting me to volunteer for something like that again.”

Oh I don’t know, I’m sure I can think of something to entice you out there,” John said with an intense look before reaching out giving Rodney’s shoulder a squeeze. It was the most physical display of affection either would allow in public as they were both very private people. “Now go on.”

Rodney let himself be sent on his way. Upon entering the lab all eyes went to him.

He sighed. “They’re in discussion about what to do,” he told them.

Radek muttered something impolite sounding in Czech. “Would be stupid fools to send you away, both of you. You are needed here.” He pointed a finger at Rodney. “Do not let that go to your big head. I just don’t want to be stuck with your job permanently. Too much paperwork.”

Thanks, it’s nice to know you care,” Rodney said dryly. Then he swallowed as he realized that they really did care, that they had just spent the last few days proving it. “No, I mean it, thank you, all of you, for your words and your support the last few days. It means a lot, even if the delegation decides against us. So, in case they do decide to remove me I just want to say-”

No,” Radek cut him off. “You save your goodbyes for when we are certain. Until then you work as if you are staying.”

Rodney met his gaze, then glanced at the rest of the scientists present. “Alright,” he agreed. “In that case, enough with all this emotion. We’re here to do science so get back to work, you slackers.”

And we wanted him to stay, why?” Simpson muttered as she turned back to her computer but she was smiling as she said it.

Rodney ignored the sounds of everyone going back to work as he settled himself down in front of a computer to catch up on the readings and reports from the last few days, seeing as the interviews with the delegation had kept him from doing any real work.

He frowned as he noticed something odd. “What’s this?” he asked, calling Radek over and pointing it out to him.

Radek blinked at it. “We haven’t identified the program yet. It came online when we brought up some of the dormant systems.”

Hmm.” Rodney began typing, trying to identify the program. His eyes widened as the computer responded, bringing up the schematics for an Ancient ship.

Radek stared in shock. “Is that - ?”

It is,” Rodney breathed out. “I have to show this to Elizabeth and Sheppard, immediately. We have to go investigate. Do you know what this could mean for the expedition? What we could find on a working Ancient warship?” He kept his voice low as he shared a glance with Radek.

But the delegation won’t allow you to go,” Radek pointed out.

Rodney’s face fell before a determined look crossed his face. “It has to be us,” he stated firmly. “You know I have the best chance of getting the systems working after 10,000 years and if anything needs to be activated Sheppard is our best bet, even after the change to his DNA he still has the strongest gene. And this could be our chance to prove to the delegation that we can still do the work we came out here to do.”

Radek nodded at him. “Good luck then.”

Rodney was already reaching for his radio. “Dr. Weir?”

Yes, Rodney, what is it?”

I need to speak with you and Colonel Sheppard immediately in your office.”

Rodney, I’m not sure this is the time for us to be having a meeting. Can’t this wait?” He could hear the frown in her voice.

No, this is urgent. We’ve found something, something huge.”

Alright, my office. Ten minutes. I’ll contact Colonel Sheppard. Weir out.”

Rodney closed the connection on his end and reached for the laptop, saving the work before closing it, picking it up and speeding out the door.

The Aurora just might be the answer to their prayers.

Chapter Text

John watched as Rodney set the laptop he was carrying on Elizabeth’s desk and quickly pulled up the program he had found earlier, showing a blip in an area of space.

What is it?” Elizabeth asked after looking at it for a moment.

That is the signature of an Ancient ship called the Aurora. With the ZPM now powering the city, we've been reactivating dormant systems. This particular system tracked the location of Ancient ships during the war.” Rodney minimized the window and pulled up some schematics. They were incomplete but gave an idea what the ship looked like.

A warship?” John asked, perking up in interest.

Oh, see, look at his eyes, all lighting up again. It's Pavlovian.” Rodney rolled his eyes. But his tone was fond and he had a faint smile on his face as he looked at John. “I crosschecked the logs. They were on a reconnaissance mission.” He switched windows on the computer again. “When we activated the ZPM, the city must have sent out some kind of an automated subspace beacon, recalling ships back to Atlantis.”

Even Elizabeth was looking interested now. “How long before it gets here?”

Rodney sighed. John recognized it as one of his frustrated sounds. Obviously, they were missing something here. Rodney proved him correct when he opened his mouth again. “Well, given that it's at the edge of the Pegasus galaxy… Let me see, carry the four… 42 million years. Should we go wait on the porch?”

John smirked at the sarcastic, scathing tone. It was nice to see Rodney getting back to his normal self after having to deal with the delegation but he couldn’t believe Rodney had missed the obvious solution. “So we take a jumper through the nearest Stargate and check it out.”

Clever, but wrong.”

Oh, he had already thought of it. Which meant.. John grinned. “There are no nearby Stargates.”

Not within jumper distance, no,” Rodney confirmed.

Which leaves us only one way to get there,” Elizabeth said, looking thoughtful. “You do know that even if he agrees we would still have to get approval from the delegation. Neither of you are currently cleared to leave the City.”

Rodney groaned. “Do we really need to tell them?” he asked. “Couldn’t we just go, find the ship and then come back? Prove to them that we can still do our jobs?”

Elizabeth stared at him. “Rodney, you said the ship was on the edge of the Pegasus galaxy, how long do you think it will take the Daedalus to get there?”

If we push the engines, maybe five days.”

John got her point first. “Do you really think the delegation won’t notice us missing for that long? What if they come to a decision or just decide they want to speak with us again? Any chance, slim as it may be, we have of remaining here would disappear if we left without telling them.”

But they’re not going to let us go! And it has to be us,” Rodney insisted. “And it would be a bad thing if they decide to wait on this. Really bad. I’m not sure that we’re the only ones capable of receiving that signal.”

You mean the Wraith might pick it up,” John said, suddenly feeling the urgency of the situation. They really did need to go, and quickly. “Elizabeth,” he started, turning to her.

Leave it to me,” Elizabeth told them. “I’m sure I can persuade them to allow you to go, even if they agree to it just to see you fail. Which you won’t,” she stated firmly before Rodney could protest the idea of them failing

John recognized that glint in her eyes. It was the same one she’d had right before going to negotiate with the Genii for nuclear weapons. He almost felt sorry for the members of the delegation. He paused, thinking about that for a second. On second thought, no, he didn’t. He wished he could be a fly on the wall for that meeting. With popcorn.

Snorting at that mental image, he gently slapped Rodney on the back. “Come on, I’ll help you gather whatever you think we’ll need while Elizabeth goes to ‘talk’ with the delegation. We’ll get Ronon and Teyla to help.”

He grinned as Rodney immediately launched into a rant about delicate equipment and bumbling cavemen as they left the office, leaving Elizabeth shaking her head in fond amusement behind them.


General Jack O’Neill had a headache. God, he hated dealing with politicians and that’s what this whole inquiry basically was. He didn’t see what the big deal was in letting Sheppard and McKay continue to do their jobs. But Woolsey, that stickler for rules, kept hemming and hawing, plus he had to put up with Chapman and Ellis and their bigoted views. How the hell had Ellis made it this far into the program? He was definitely going to have to check into what was going on with those in charge of screening candidates for the program. And he couldn’t tell what was up with Wray. One moment she seemed to be agreeing with him, the next she would be against him.

A chime at the door ended the loud argument from Ellis, and Jack was grateful for the reprieve, however brief, from the yelling. Mentally signaling the door to open, and he would never get used to that, he was surprised to see Elizabeth and Colonel Caldwell on the other side.

Woolsey beat him to the punch, gesturing them into the room. “Dr. Weir, Colonel Caldwell, is there a problem?”

Not a problem, but I thought you would be interested to know that Dr. McKay has located an Ancient ship, named the Aurora, at the edge of this galaxy.”

Jack perked up in interest at the news. “Oh?”

Yes, one of the dormant systems we activated recently found it. I’d like for the Daedalus to go check it out as it’s too far from any Stargate for us to reach otherwise.”

I don’t see anything wrong with that,” Woolsey stated. “But why are you asking us? Something like that isn’t something we need to approve.”

I’d like Colonel Sheppard and his team to accompany them.”

Ah, now Jack understood why she had come to them.

Absolutely not!” Ellis burst out, as expected. He turned to the rest of the delegation. “You can’t be considering this! This is why this expedition needs a strong military commander in charge of the whole operation! Someone who knows how to think tactically instead of a weak civilian.”

In either case, that military commander wouldn’t be you,” Wray cut in, glaring at him. “Your attitude has shown you to be too bigoted and small minded to be in charge of a base like this. The number of potential allies you would offend and drive away is too great. If I have anything to say about it you will never gain command of this outpost.”

Ellis bristled in anger.

Woolsey cut in before he could say anything else. “We have not yet made a decision, Dr. Weir. It would be premature to allow Colonel Sheppard and Dr. McKay to leave the City just yet.”

I know you haven’t made your decision yet. But until you do they are still members of this expedition. And they have the best chance of succeeding in this task. There is no one with more knowledge or experience than Dr. McKay when it comes to Ancient technology, he is our best chance of getting that ship operational again in a timely fashion. And if anything needs to be initialized, Colonel Sheppard’s gene is still the strongest.” She leaned forward over the table. “Look, if you have to, then think of it as a test to prove that they can still do their jobs.”

Hmm.” Woolsey looked thoughtful. “What is your opinion of this, Colonel? You’ve been very quiet since you arrived.”

I think it is extremely important that we see if this ship is salvageable,” Caldwell started. “I think my crew is up to the task but, as Dr. Weir pointed out, we lack the experience in dealing with this technology. I agree with her that our best chance would be to utilize Colonel Sheppard’s and Dr. McKay’s skills in this task.”

I’m all for it,” Jack added. “We can just hang out around here for a few days while we wait to see if we gain another ship.” He gave Elizabeth a serious look. “How’s the fishing here?”

Woolsey ignored his last comment. “Very well,” he agreed, ignoring Chapman and Ellis’ protests.

Thank you,” Elizabeth said before turning to Caldwell. “Well Colonel, I guess you should go see about getting your ship and crew ready while I go check in on my team.” With that, the two left.

Jack groaned as another chorus of arguments began as soon as the door closed behind them.


John led his team through the Aurora, all of them clad in orange space suits. “Look, the first priority is going to be getting the life support up. We only have a limited time in these suits. Next priority is going to be assessing weapons and getting them up and running.”

What? No, that is not the second priority,” Rodney disagreed. “You and your weapons fascination. There are so many other systems that are just as, if not more important-”

John cut him off. “Rodney, we already had an encounter with one Wraith vessel. It might have been a scout and easily taken out but that doesn’t mean it didn’t signal any other Wraith vessels before it got here. We have to be prepared for a fight if more of them show up. We can’t only rely on the Daedalus to defend us.”

Oh, I didn’t think of that.” Rodney sounded a bit sheepish, a bit scared. “I guess shields and the engines are next on the list,” he added as they came to what must be the bridge. “Oh no.”

John agreed with the sentiment. The front view screen was broken and the whole room was open to space. “Can you bypass this room?” If not they would have to remain in their space suits to do anything important.

Maybe, there must be an auxiliary control room around here.”

Colonel Sheppard,” Teyla called.

They turned to see what she had found, a room full of stasis pods, each with human-looking beings inside.

Ancients, real Ancients,” Rodney breathed out excitedly as he moved to examine a pod. “The stasis pods are still active and powered up. They’re alive.”

Stasis?” Ronon asked.

John ignored Teyla’s explanation as he stepped up beside Rodney who was examining one pod in particular. He pointed at the elderly man inside. “Look, this one’s uniform is different than the others. He must be the captain.”

Or the maitre d',” John muttered, watching Rodney check his scanner and talk about life signs and the Daedalus’ sensors.

Look at all of them,” Teyla said, gazing at the large number of pods. It was obvious she was in awe of coming into contact with those she referred to as Ancestors.

That’s just on this deck,” John pointed out. “Who knows how many more there are on the rest of this ship.” He turned to Rodney. “I know this is exciting for you but priorities, remember?”

Rodney nodded. “I’m on it.”

A short time later life support was restored with the bridge sealed off. John sighed, feeling glad to be out of that suit. “Okay, good job Rodney. How about weapons?”

The scientist tapped at something on a console before his face fell. “There’s not enough power.”


Well that’s not quite true,” Rodney started. “There is power but it would mean turning those off.” He gestured back toward the stasis pods. “Those things are big energy hogs.”

Teyla looked up sharply at that. “You cannot.”

John looked at her. “Teyla, we don’t know when we might have more company of the Wraith variety. We’re dead in the water here, we need to get systems up and running and we need power to do that.”

She glared at him. “You would be murdering who knows how many helpless individuals, the rightful owners of this ship.”

If the Wraith come back they’re all dead anyway. And it’s not like we can take them out of their pods, remember Old Weir? They’ll die if we do that.” He sighed. “Look, I’ve got to update Colonel Caldwell on what we’ve found so far. Why don’t you and Ronon explore the ship, I promise we won’t take any action just yet.”

She gazed at him, weighing his words before giving a sharp nod of agreement.

John sighed again as he initialized a connection to the Daedalus and explained what they had found.

They’re all alive? The entire crew?” Caldwell sounded incredulous and John couldn’t blame him.

Well, they're in a kind of suspended animation.”

Not entirely suspended, however. The pod has slowed their aging considerably, but the bodies are virtually moribund,” Rodney added from where he had connected his laptop to a pod and was examining the system.

John glared at him for abandoning working on the ship’s systems but then there really wasn’t much he could do without power. “Teyla and Ronon are searching the rest of the ship. My guess is there's hundreds.”

Is there anything we can do for them?” Caldwell asked.

Well, reviving them is out of the question. The pod’s the only thing keeping them alive,” Rodney informed him. John watched him frown at something on his computer before continuing his report. “The pods are drawing too much power from the ship’s systems for us to access weapons, shields and engines. It’s a bit of a dilemma. Do we turn off the power to the pods in order to save the ship, or leave them all to die when the Wraith return?” His computer beeped. “Wait.”

John turned to look at Rodney. “What?”

Rodney was getting excited. “There's something going on. This pod is magnetically shielded. I'm reading cortical signals.”

Which means?” John asked.

A technical explanation followed but what John took away from it was that the crew were communicating with one another while in stasis. He and Caldwell asked a few more questions, receiving Rodney’s unique brand of sarcasm in response, especially when they asked him about communicating with them.

Rodney sighed. “Being able to communicate with a living Ancient is the opportunity of a lifetime, but this system is a highly complex system, which I will have— Wait a minute.” He ignored John’s question to radio Teyla. “Have you found any more of those pods.”

Yes. Many. And there are many more decks we have yet to search.”

Are any of those pods empty?” Rodney asked.

John didn’t like where this was going.

A few,” Teyla responded.

Perfect,” Rodney said, shooting John a look.

Yep, John really didn’t like where this was going.

A few minutes later found the whole team gathered around one of the empty pods. John eyed it doubtfully. “Are you sure this is a good idea?” he asked as Rodney opened the pod, a platform sliding out of the wall.

You can’t really be proposing actually freezing yourself in one of those things?” Caldwell added over the radio.

I should be able to tap into the neural network without actually initializing stasis.” Rodney looked up from his work, obviously sensing their hesitation. “Look, it won't take long. I'll be in and out.”

John gave him a dubious look.

Rodney huffed in irritation. “Look, the quickest way to figure out what is going on in there is to tap into the system and communicate directly with the Captain. Need I remind you of the obvious value in this? Not only what we can learn from them but, beyond the power situation, I’ve hit a bit of a snag in gaining access to some of the systems. They’re locked down via an access code. I could eventually hack the system but it’s easier to just ask the Captain for the code.”

And you think he’s just going to hand it over to you?”

Well, if I explain things,” Rodney looked uncomfortable. “Plus they deserve to know that the Wraith could be on their way so they can make a decision about what to do with the ship and the pods.”

John’s eyes widened at that. Rodney was actually suggesting asking the crew to effectively commit suicide in order to save the ship. John couldn’t let him be the one to do that.

I’ll be in and out,” Rodney repeated.

But is it safe?” Teyla asked.

John latched onto that. “Yeah, I don’t have a good feeling about this, McKay.”

Rodney shot him a hurt look. “What’s the matter, Colonel? Don’t trust me?”

With my life, yes, with yours, no,” John told him without missing a beat. “Which is why I’ll be the one to go in.”


John shrugged. “Better to have you on the outside in case something goes wrong.”

It won’t,” Rodney protested.

But if it does,” John said, taking off his vest.

But it won’t! How many times do I have to go over this?” Rodney asked, casting a worried look in John’s direction.

Rodney,” John said softly, reaching out to touch his cheek. Rodney quieted instantly, leaning into the touch. “On the off chance that something does happen which of us is in a better position to ensure the other’s safety?”

A short time later found John reclining on the platform, listening to Rodney explain the system to him. “Now, when I close the lid, the pod's systems should activate. Ready?”

I was,” John responded, unable to resist tweaking Rodney’s nose a little.

Good,” Rodney said, moving to activate the pod.

And while you’re monitoring me you can also work on some of the repairs in preparation for me getting the access codes,” John told him.

Yes, fine,” Rodney said, pressing something on the pod. “And here we go.”

A thought hit John. “Wait, what if they react negatively to my appearance?” he asked. But it was too late and the pod slid into the wall, closing around John.

John blinked as he opened his eyes in a brightly lit corridor that he recognized as an undamaged version of the Aurora. He looked down at himself to find he was wearing a white uniform similar to that of those in the stasis pods. He did a double take as he gazed at his arms before strongly thinking disconnect.

What? What’s wrong?” Rodney asked, worry in his voice as the pod opened and John sat up, looking down at his body.

I was me again,” he responded, taking in the blue scales of his arms and hands. He wasn’t sure how to feel.


I opened my eyes and there was no blue, no scales, just human John Sheppard.”

Oh, is that all?” Rodney asked, giving a sigh of relief. “That’s because the system accesses your mental image of yourself and that’s the way you still view yourself.”

Oh.” He glared at Rodney. “You could have mentioned that beforehand.” Guess he wouldn’t have to worry about the crews’ reactions to him after all.

Rodney waved him off. “Now are you ready to try again? You’re the one who said we don’t have much time.”

John sighed and laid back down, letting the stasis system activate again.


While John was talking with the Aurora’s Captain, and hopefully getting the access codes, Rodney radioed the Daedalus and arranged for the supplies he had gathered on Atlantis to be beamed over along with several technicians and a nurse from the Daedalus’ crew. He pointed at the nurse. “You are going to monitor the Colonel’s EEG pattern, if anything, and I mean anything, I don’t care how small, changes you are to notify me immediately. Do you understand?”

She wilted under his glare and agreed.

Satisfied he turned to the technicians. “It’s our job to repair as much of the damage to the critical systems as possible as quickly as possible.” He started assigning tasks. “Now this technology is different from what you’re used to working with. If you’re not sure; ask. Do not assume that it works the same way as what you’re used to or you’ll likely blow us all up.” He sent them on their way while setting up a monitoring program on his tablet to keep him informed of their progress while he went to begin his own task, the weapons system, as he had deemed Novak sufficiently competent to deal with the engines.

He sighed as he reached the armory and found it depleted of drones. Typical. However, upon further investigation of the ship’s system he discovered a secondary weapons’ system, kind of like a phaser bank. He noted the inefficient design that made it a huge power drain, which was probably why they hadn’t found something similar before.

He set to work examining and repairing the phaser bank to the best of his abilities, glad he had the foresight to bring along various crystals and other replacement parts from Atlantis. He hadn’t gotten far when he received a call from the nurse he had left monitoring John and he abandoned his work to race back there.

He got back there just in time to see the pod sliding out and the canopy opening. “So?” he panted as John sat up.

It worked.”

Rodney rolled his eyes. “Of course it worked.” John started to sit up and Rodney reached out to help him. “Were you able to communicate with the Captain?”

Face to face. Pretty impressive in there. They have a whole virtual reality thing going on.”

The term is virtual environment .”

Yeah, whatever.” John rolled his eyes. “Anyway I have to go back,” he said as he reached for his radio and contacted Caldwell.

You didn’t get the access code,” Rodney stated.

Not yet,” John admitted before launching into an explanation about what he had found in there and about the communique the Captain was carrying about a possible Wraith weakness.

Rodney listened as Caldwell agreed with John that it was necessary that they retrieve that information. As John readied to reactivate the pod Rodney reminded him not to forget about the access code.

He watched John for a few moments before returning to his previous task. Again, he hadn’t been working long when he was interrupted, this time by Caldwell.

Dr. McKay. Long-range sensors have just detected two Wraith cruisers heading this way, no doubt coming to investigate why their scout ship was destroyed earlier.”

Oh, that so wasn’t good. “What’s their E.T.A.?”

A little over an hour, and I plan on being long gone by then. What's the status there?”

I’ve made some progress on a secondary weapons system but it’s a power drain and I need the access code to activate it. I’ve been keeping track of your technicians and they’ve been doing an adequate job with the engines but the hyperdrive is shredded. We won’t be able to open a hyperspace window.”

And Colonel Sheppard?”

He’s still in the pod,” Rodney confirmed.

Caldwell sighed. “Understood. Just be aware of the time constraints with the Wraith ships approaching. We can't risk being discovered.”

Yes, yes, yes, yes, yes. Ticking clock. Anything else?”

If he's not out of there in thirty minutes, disconnect him manually. As much as it would pain me to lose a ship like the Aurora and the information about the Wraith’s weakness, we can’t risk being discovered,” he reiterated.

Right,” Rodney said, worry filling him. ‘Hurry up John,’ he thought as he threw himself back into his task.

A call from Teyla and Ronon pulled him from his task a third time and then there was the knowledge that there was a Wraith in stasis accessing the same system as John. Then he was called back by the nurse who informed him that John had exited stasis only to return a moment later. He didn’t know what the Colonel was playing at but he was going to have some words with him about that later.

Then it was back to the Daedalus to brief Caldwell in person. And being told they only had 15 minutes to do what they could and retrieve John or Caldwell was going to beam them all out and destroy the Aurora to prevent the Wraith from getting it. Just your typical day at work, really.

All of this ended up with Rodney going into the system himself to track John down, leaving Teyla behind to monitor and manually disconnect them if necessary. He hoped it wouldn’t come to that.

Once inside the virtual environment, he had his own moment of disconnect at seeing his fully human appearance. He quickly shook it off as he went in search of John. He probably shouldn’t have been surprised to find him in the brig.

There you are,” he said as he was unceremoniously pushed into the cell with him. “What are you doing in here?” He blinked as he gave John an appreciative look, now understanding John’s earlier shock. Rodney thought that it was good to see the old John but if he was honest with himself he was missing the blue and the scales. He noticed John eyeing him similarly and wondered if he felt the same.

I was about to ask you the same thing,” John said, sounding annoyed.

I came to help you.”

Oh. Well, I feel better already.” The tone was sarcastic but the look he shot Rodney showed he was sincere.

Rodney was glad to learn that John wasn’t having any problem disconnecting from the system and he quickly explained about the Wraith, which John deduced to be masquerading as the First Officer, and Caldwell’s demands that they get out of there so he could destroy the Aurora.

John hissed angrily at the news. “That’s such a waste. Why?”

Rodney told him about the Wraith ships on the way.

John closed his eyes. “Oh. Yeah, that makes sense then. But it’s still a waste.” He pinned Rodney with a look. “You’re sure there’s no way to save the ship?”

Well, I did find a secondary weaponry system that I think will take out the Wraith ships but it’s a power drain. Huge power drain. And I need the Captain’s access code. I definitely do not have time to hack into the system and make a workaround.”

What about getting the Aurora out of here? If there are two Wraith ships coming now, more could also be on the way.”

We’ve made some progress on the engines but there’s no way we could open a hyperspace window.” Rodney frowned, thinking. He started snapping his fingers. “Or at least the Aurora can’t. But if the Daedalus makes a big enough one we could fly the Aurora through it, maybe not all the way to Atlantis but at least close enough to a planet with a Stargate so we could do more repairs.” His face fell. “The only problem is that a hyperspace window that big would be obvious to anyone who came to this area of space and easy to track.”

John frowned. “What if we masked it somehow?”


John smiled. “By blowing up the Wraith.”

Rodney frowned again then snapped his fingers and pointed at John. “Yes! That could work. The timing would have to be perfect though. We’d have to enter the hyperspace window just after destroying the Wraith ships so that the shockwave would destroy any signs of the hyperspace window.” He sobered. “You do know that doing this will kill the crew of the Aurora? There won’t be enough power otherwise.”

John nodded grimly. “They’re dead either way. I think if we explain everything to the Captain he’ll go along with this plan.” He glanced at the cell. “But first we have to get out of here.”

Hold that thought,” Rodney told him before concentrating on disconnecting. Once out he ignored questions from Teyla and Ronon as he worked on his tablet, pausing just long enough to tell them to keep stalling Caldwell before reentering the system.

He arrived to find the cell door open and two guards unconscious on the ground in front of it. “Rodney, you’re a genius,” John said, grinning at him.

Thanks,” Rodney replied, as they grabbed the guards weapons and control devices. They made their way down the corridor, hiding when they spotted a group of people in the corridor ahead of them.

That’s her,” John said, pointing at a beautiful blonde woman.

That’s the Wraith?” Rodney asked, shocked. “Wow, she’s hot. I mean seriously hot.”

That earned him a glare from John. “You’re drooling over a Wraith.”

I know. I disgust myself sometimes.” He caught the glare John was sending his way. “But looks aren’t everything. Anyway, you’re hotter.”

John preened momentarily. “Come on, I have to get to the Captain.”

They were passing a terminal when Rodney snapped his fingers. “Oh! That communique you were interested in. I should be able to access it from here. Then you only need to worry about getting the access code from the Captain.”

Really?” John asked, expression brightening.

Yeah, just give me a minute,” Rodney said absently as he accessed the terminal. His face fell. “Uh oh. It’s gone. It looks like the Wraith erased it.”

Then why is it still in here if the message is gone? Why didn’t he end the program? What’s the point of continuing it?”

Rodney thought about it for a moment then paled. “Oh no.” He turned to John. “You said they were trying to modify the hyperdrive. According to the Atlantis database, there are two different types of Ancient hyperdrives. There's the more basic, interstellar kind, like the one the Aurora has, and then there's the more powerful, intergalactic kind similar to the one the Asgard provided us for the Daedalus.”

John frowned at him, obviously not getting it yet. “Why would the Wraith want to soup up the Aurora’s hyperdrive?”

Because the Wraith hyperdrives are nowhere near as advanced as the Ancient hyper-drives. With all of the technology the Captain is feeding her right now—“

Rodney saw the moment it dawned on John’s face. “She'll learn how to modify the Wraith's hyperdrives from interstellar to intergalactic. They’ll be able to make it to Earth.” John’s face hardened. “That’s what this has all been about, their new feeding grounds.”

Even if she doesn't have all the information she needs, we need to stop her from sending what she's learned so far to the Wraith ships that are on the way.”

Can you disconnect her?”

Him and not from the inside, no. But I should be able to disable the pod interface from the outside.”

John glared at him. “Then why didn’t you?”

Rodney glared right back. “Because I didn’t know what that would do to you!”

Well, that's very thoughtful of you, but now she knows all about Atlantis.”

You told her?” Rodney gaped at him incredulously, crossing his arms over his chest as his gaze turned suspicious. “Why?” he asked accusingly.

Oh don’t look at me like that. I did it because I was trying to convince them that— Just go and unplug the Wraith while I talk to the Captain. Then get everything ready for our plan.”

Fine,” Rodney huffed before disconnecting.


John waited outside the bridge for Rodney to disconnect the Wraith but had to leave his hiding spot when they prepared to engage the hyperdrive. He tried to explain but of course, they didn’t believe him. Thankfully Rodney came through and the Wraith began to alternate between its current appearance and its true body before fading out altogether.

John looked at the Captain’s shocked face. “I hope that was proof enough.”

All this time, I thought we had evaded the enemy. Instead, I've been unwittingly assisting them.” The Captain looked defeated.

No, sir, she didn't succeed. And if you tell me the information in the communique, we may be able to defeat the Wraith once and for all.”

The information is in the ship's computer. I can give you my access codes.”

We checked. It's all been erased. Can't you tell me yourself?” John asked.

The Captain shook his head. “I'm afraid I was never made aware of its contents, Colonel Sheppard. The Council feared the possibility of our capture was too great. The information in that communique is gone.”

John sighed and shook his head in disappointment.

Ten thousand years… Even in stasis, our physical bodies must be…”

Very old,” John confirmed, his voice gentle. “Too old.”

The Captain sighed, looking around the bridge at his crew. “My crew deserves to know.”

Yes, they do, and I'd love to give you all the time in the world for that, but right now, there are two Wraith ships on the way.”

The Captain looked sad but determined. “We've longed for nothing more than returning to Atlantis…to raise a toast to home and victory. We may not return home but we will do whatever we can to ensure that victory. For that, I will need your help.”

John listened as the Captain explained his plan. “That would work to take out these two cruisers but what about a bigger victory?”

What do you mean?”

Rodney, one of my scientists found your secondary weapons system. He thinks with your access codes he can use it take out the Wraith before using our ship to create a big enough hyperspace window to take the Aurora through. The only issue is power.”

The power drain would deactivate our stasis pods, killing us,” the Captain finished.

Look, your own plan calls for you to sacrifice yourselves. But is it also necessary to sacrifice the Aurora? The Wraith have had the run of this galaxy for 10,000 years. We’ve made some progress in striking back and taking them out but we could do so much more with this ship. Please.” John pleaded, hoping the Captain could see how desperately they needed the Aurora in his face.

The Captain eyed him for a long moment. “You’re right. Either way, I and my crew won’t survive this. But a bigger blow to the Wraith, a bigger victory, that is something we can grant. Here,” he said before reciting his access codes for John. “May I ask a favor? One commander to another. Remember us.”

I will. Once we’ve returned to Atlantis we’ll toast you and your crew.”

Not the homecoming we expected or hoped for. But we shall soon return home, victorious in death at least.”

Thank you,” John told him sincerely, offering him a salute.

The Captain looked confused before nodding at him. “Now go. And bring victory to the Aurora.”

John concentrated and found himself back in the pod as it opened. The first thing he heard was Rodney’s voice, even before he opened his eyes and sat up.

It’s about time. What did you do, stop to play a round of golf? We’ve got serious problems!”

What happened?” John started to ask before his eyes widened. “Get down!” He drew his pistol and fired at the Wraith coming up behind Rodney. He hit it multiple times and it collapsed. Rising to his feet he approached it, weapon drawn as Rodney did the same.

That happened,” Rodney said dryly. “Not so hot now.”

The Wraith sneered at them. “Our ships are coming. They will retrieve what I have learned. Earth will soon be ours.”

Not if I can help it,” John said before firing again, this time killing the Wraith.

The radio activated. “Colonel Sheppard, we’re reading two life signs. I hope that means what I think it means,” Caldwell said.

John looked at Rodney, eyebrow raised in question.

Everything’s ready,” he confirmed.

Sheppard, we’re out of time, we have to blow that ship.”

No, there’s another way. Get Hermiod and Novak on the line for Rodney to explain,” John told him over the radio as he and Rodney headed for the auxiliary control room and the chair there. “We can take out the Wraith and still salvage the Aurora.”

The Wraith ships are almost here. There’s no time.”

John dropped into the chair, gratified that it activated instantly. He glanced over and saw Rodney working on his tablet while talking fast into his radio. “We don’t need any more time. You have to turn the Daedalus away like you’re running away.” He closed his eyes and mentally provided the Captain’s access codes but kept everything powered low so that the Wraith wouldn’t detect anything.

What? Have you lost your mind?!”

Just don’t go too far. You’ll need to be close for the Aurora to use your hyperspace window to escape the destruction of the Wraith cruisers.” John watched the feed the Aurora provided of the Daedalus beginning to turn away as the cruisers approached the apparently derelict Aurora. He nodded in satisfaction as the Wraith fell for the deception, ignoring the apparent retreat of the Daedalus to focus on the Ancient ship. He glanced at Rodney, waiting for the confirmation that they were close enough.

Rodney was completely focused on his tablet. “Now!”

John closed his eyes, brought the weapons system online and fired. “Now, Daedalus! Hyperspace window!” He saw it forming and nudged the Aurora to fly through it, following the Daedalus before the shockwave could reach them.

Systems are holding steady,” Rodney said, studying the readouts. The lights had dimmed but everything still seemed to be working. “Except for the stasis pods,” he added grimly.

John nodded, acknowledging the sacrifice of the crew of the Aurora. “We’ll raise a toast and see that they get a proper goodbye when we reach Atlantis. At least they’ll finally make it home.”

Yeah,” Rodney said, his expression saddened.

The radio crackled. “I don’t know how you pulled it off but excellent work Sheppard, McKay,” Caldwell said, his voice full of shocked awe. “Hermiod tells me we won’t be able to keep this up for long but we’ll reach a system with a Stargate soon enough so that we can safely repair the Aurora’s hyperdrive. Once that’s done you’ll be able to bring her and her crew home.”

John nodded. He sent a silent thank you to the Captain and his crew for their sacrifice. They would all be home soon enough.

Chapter Text

John and his team stepped through the Stargate into Atlantis to the accompaniment of cheers. He blinked as he looked up to see Elizabeth standing with the members of the delegation. Ellis and Chapman looked sour as ever but O’Neill was grinning and even Woolsey and Wray looked happy to see them.

Colonel Sheppard, Dr. McKay, good to see you again,” Woolsey said. “We’ve heard Colonel Caldwell’s report. I understand that our new acquisition is entirely your doing.”

We couldn’t have done it without the sacrifice of its crew,” John corrected. They had left the Aurora safely behind on the planet whose Gate they had just used, the Daedalus remaining to protect it until they could get a team of scientists and engineers out there to make the necessary repairs to return it to Atlantis.

Yes. It would have been nice to be able to converse with an actual Ancient,” Elizabeth said, somberly.

Yeah, speaking of, I promised to bring them home so I would really like to get a team together so we can get started on those repairs.” He turned to Elizabeth. “You think you could find something about their burial practices in the database? I didn’t have a chance to ask what they wanted.” At her nod, he continued. “Then we’ll just go arrange that repair team.”

Before you do that Colonel, there is the matter of our decision on your posts,” Woolsey interjected.

John felt his heart sink and Rodney stiffened beside him. “I gather you’ve reached one?” He couldn’t read any of their faces.

Woolsey cleared his throat. “Yes. You have engendered a tremendous degree of loyalty in the members of this expedition. In light of their answers and support, as well as your actions with regard to the Ancient ship Aurora, we feel that the two of you have proven yourselves capable of carrying out your duties. However,” Woolsey held up a hand to prevent anyone from saying anything, “this decision was not reached lightly. You should expect your decisions to continue to be scrutinized for the foreseeable future.”

John didn’t care about that last part as relief flooded through him. He was elated. Not only was he staying on Atlantis, with Rodney, but they were letting him keep his command. “Thank you,” he managed to choke out.

The room filled with cheers again as everyone present learned that he and Rodney were staying.

O’Neill calmed it all down by clearing his throat. “With this latest stunt, you two have more than earned your places here.” He tilted his head. “So is there an estimate on how long it will take to repair the Aurora?”

Yes, we should get the ship back to Earth as soon as possible,” a sour looking Ellis added, earning glares from almost everyone present.

Well, I would estimate at least a week before we can repair it enough for a return trip to Atlantis. But I couldn’t really say more until we get it here for more complete repairs. Frankly, I’m not sure I would trust it with an intergalactic journey, even fully repaired. It’s just too old, has sustained too much damage, and there’s not enough of the right parts for repairs,” Rodney informed them.

So you’re saying it can’t be done?” Chapman spat in disgust.

Look, it’s the same problem we’ve faced with Atlantis. Too much damage and not enough parts. We can scavenge and re-purpose items so that the equipment will work but it probably won’t match the standards of the original. We’re still learning about this technology and how it works. We don’t know enough to build our own parts. Yet.”

But you think it will be safe for interstellar travel?” Wray asked.

Once we’ve repaired it, then yes.”

O’Neill clapped his hands. “Then I guess, at least for now, Atlantis has gained a ship.” He glared the other members of the delegation as they looked at him unhappily. “Don’t look at me like that. If they have a ship of their own it’ll free up the Daedalus for more use back in the Milky Way.” He turned to Elizabeth. “I think we’ve taken up enough of your time. Thank you for showing us your City but we’ll go pack and then we’ll be heading back to Earth. Things to do there, I’m sure the work has just been piling up while we’ve been gone.” He shook her hand then turned to John and Rodney. “Sheppard, McKay, keep up the good work,” he told them. With that, he turned and led the rest of the delegation out of the Gate Room.

Once the doors closed behind them the room once more erupted into cheers. John and Rodney found themselves the recipients of a multitude of congratulations and back slaps.

Elizabeth stepped forward and gave them each a hug. “Good work, I knew you could do it,” she told them. “Now go, I’m sure you’ve got things to do.”

So they left. John accompanied Rodney to his lab watching as the scientist ordered around his minions and made decisions on what they needed to bring to the Aurora for repairs, selecting who would go and what tasks they would perform. Once John got an idea of how many scientists and engineers would be needed, he contacted Lorne to arrange for the accompanying military escort and jumpers.

After being at it for a few hours they got a call on the radio from Elizabeth. “I thought you’d like to know the delegation has left.”

John breathed a sigh of relief. He liked O’Neill, and Woolsey and Wray hadn’t been too bad but he was glad to have Ellis and Chapman off of his city. It also meant that it was too late for them to change their minds.

I’m sure you two haven’t eaten yet, join me for lunch in the Mess?” Elizabeth asked.

John blinked, he hadn’t realized how much time had passed. “Yeah, that sounds good.” He ended the call and got Rodney’s attention. “Come on, let’s go eat. Elizabeth wants to talk to us over lunch.”

It’s that late already?” Rodney asked, saving his work. “What’s she want?” he asked as they started heading toward the transporter.

John shrugged. “She didn’t say.” He grimaced as he caught his reflection in a panel.

What’s wrong?”

Nothing,” John replied, shaking his head. “Just got to get used to my reflection again. It was nice seeing the old us, even if it wasn’t real.”

Rodney gave him a thoughtful look but didn’t say anything as they arrived at the Mess. They entered to cheers and applause. It looked like it was time for another round of congratulations.

He accepted them good-naturedly and could tell Rodney was touched by the display. He noticed the glasses of champagne Elizabeth must have arranged and accepted one. He held up a hand and the room quieted.

Thank you. I’m going to keep this brief. First, thank you all for your support with the delegation. It means a lot to both of us. I’m sure that without your trust and support they would have reached a very different decision. So thank you, all of you. Last but not least, I’d like to raise a toast.” He lifted his glass and waited until everyone had one. “This might seem a little strange but I promised to do something when we got home. To the crew of the Aurora.” They all clinked their glasses together and drank.

The rest of the party was spent accepting congratulations from those present. If John noticed Rodney being a bit quieter than usual or looking thoughtful he just put it down as the scientist thinking of the work needed to be done to get the Aurora back in working order.


You’ve been avoiding me,” John said, startling Rodney into banging his head on the access hatch he was half inside.

Ow.” He glared at John as he pulled himself out of the hatch. “Don’t you have better things to do than sneak up on busy scientists?” he asked. “And no, I haven’t been avoiding you. I’ve just been busy.” It wasn’t quite a lie but it wasn’t the whole truth either.

Rodney.” Now John was giving him a sad look as he took a step closer. “Come on, just tell me what I did wrong?”

Rodney sighed, caving in. He couldn’t take the dejected look on John’s face. “You didn’t do anything. I really have been busy.” He reached into his pocket. “I wanted to wait until I was done but I’ve only been able to work on it in my spare time which isn’t much. It’s why I haven’t been around lately. I’ve either been working on the Aurora or this.” He handed the pocket-sized device to John.

John frowned down at it. “What is it?” he asked as he turned it over in his hand, causing it to project an image of pale skin over the blue of his hands. “Rodney?!” he asked in shock.

You know those holograms we’ve found? I pulled a few of their projectors and studied them, combining that with what I knew of a Mimetic imaging device I studied briefly when I worked at Area 51. Once it’s finished it should be able to project an image of our old appearances right over our new ones, hiding our differences. I’m having trouble with the power supply but I think if we wear long sleeves and just use this over exposed areas like our faces and hands it should work. But we couldn’t wear it full time, just when we’re on a mission or something.” Rodney met John’s shocked gaze and shrugged. “It’s just, I saw the faces you’ve been making every time you’ve caught your reflection since your experience in the virtual environment. Plus you’ve been moping since Lorne started going out on the missions we used to take. I know you miss going through the Gate.”

I have not been moping,” John denied, staring at the device again. “You made me a mobile emitter.”

It is not a mobile emitter!” Rodney squawked. “It is so much more advanced-” He was cut off by John claiming his mouth in a heated kiss.

Once John pulled back, he leaned his forehead against Rodney’s. “I can’t believe you made me a mobile emitter.” He shot Rodney a heated gaze. “Are you done here?”

Rodney swallowed at the look in his eyes. “It’s nothing that can’t wait,” he managed to say, still not used to having that look directed his way no matter how many times it happened.

Good.” John kissed him again, then began towing him toward the door. “Because first, we’re going back to our quarters so I can thoroughly show you just how much I appreciate what you’ve been doing. Then later we’ll find Elizabeth and see about getting our mission slot back.”

But it’s not finished yet,” Rodney protested. “I don’t know how long it will take to get it working properly and then we still have to test it. It wouldn’t be good for it to cut out in the middle of a mission,” he couldn’t help but point out. It’s not that he didn’t like John’s ideas but there was still so much to do.

John stopped and kissed him again, pressing him against the wall so he could feel every bit of the hard body pressing against the front of his own. “I have every confidence that you’ll finish it quickly with the right incentive.” He went back to towing Rodney through the halls, uncaring of the looks they received from those they passed.

Rodney stared at him as they walked, his pupils blown wide while he nodded eagerly, all of the blood in his body rushing south. Yes, he would finish those devices in no time at all. The repairs to the Aurora could wait a little while.



John couldn’t keep the smile off his face as he tied his boots, preparing to go on his first mission through the Stargate since Elizabeth had approved the use of the mobile emitters after Rodney finally completed them. It felt good to be going through the Gate, things had been a bit too boring while he was stuck on the City. He needed to get out and do something.

And it must have been fate that Rodney had managed to complete and test the emitters just as a contact of Teyla’s had reached out with information of someone wanting to speak to them about a possible ZPM.

You’re being insufferably happy, stop it,” Rodney muttered from where he was checking his gear. “We’re about to trek through who knows how many acres of thick foliage filled with who knows what kind of creatures to meet someone who wouldn’t even give a name about a possible energy source that may or may not exist. There are much better uses for my time. There is absolutely no reason for you to be so happy about this.”

John stepped over and automatically checked Rodney’s vest straps were all in place, ignoring his attempts to bat his hands away. “Can’t help it, I’m just glad to finally be getting out there and doing something.”

And you don’t find it odd that they asked specifically for our team?” Rodney asked. “Like that doesn’t scream trap.”

John shrugged, nothing could bring down his mood today. Everything was perfect. He had his team, he and Rodney were in a good place in their relationship, he didn’t have to worry about being removed from Atlantis, and now he was about to head through the Gate on a mission. Life was good, no matter how much Rodney liked to complain. “We’ve earned a bit of a reputation,” John pointed out. “And this tip came from one of Teyla’s contacts, someone she trusts. I’m sure it will all be fine.”

Rodney glared at him. “You just jinxed us.”

John rolled his eyes. “I thought you would be too scientific and logical to believe in something like jinxes McKay. Besides, even if something does happen we can handle it. Now, are you ready or not?”

Rodney patted his pockets one last time, double-checked his holster then sighed. “Yes.”

Good, let’s go.” John led him out into the Gate Room, joining Teyla and Ronon where they stood in front of the Stargate. As Chuck began dialing the planet they would be visiting John pulled out the mobile emitter and activated it before securing it to his dog tags and tucking it safely back beneath his shirt, still amazed by the sight of his blue, scaly skin being replaced by his old tanned but pink complexion. He looked to Rodney just as the scientist activated his own emitter, his blue skin being replaced by his old pale complexion. But John knew that it was an illusion, that if he reached out to touch he would still feel the scaly skin he’d become so familiar with.

Everyone ready?” he asked as the vortex formed and the Stargate burst to life. Getting nods of agreement, he turned to look at the Control Room.

Elizabeth stood there, smiling down at them. “Go ahead Colonel, and be careful.”

John’s smile widened. “Always am,” he replied before turning and leading his team through the Stargate. Whatever awaited them there, he knew it wouldn’t be boring.