After Elizabeth's consciousness found Atlantis her only mistake had been believing her replicator companions could be trusted, but in that they proved all too 'human'. Koracen betrayed her trust, wanting to keep his replicator body so he could live for as long as it took to find a way to ascend. Although Rodney could understand the logic, he knew from his own brush with ascension that it truly was mind over matter. It was finding an inner peace and letting go of all the regrets, all the dark secrets, all of the selfishness held over a lifetime, but he doubted Koracen would have ever found that peace given a thousand years.
Technically Rodney had not lied when they sent Elizabeth through the space gate to her 'death'. She was gone, and any doubts that she was Elizabeth went with her as she willingly sacrificed herself to save the people and the city she had loved. Her replicator body, and those of her seven surviving Replicator companions would be caught by the gravitational pull of the planet being circled by the space gate, and destroyed. What Rodney had refrained from telling anyone was that he had used his compression algorithm to retain a copy of her consciousness, loaded into a virtual reality program just as Woolsey had originally agreed.
Rodney still had all the technical specs to build a flesh and blood human body for Elizabeth so he had taken over the virtual reality laboratory, situated in an unoccupied tower near the south pier, to put his plan in motion. He knew it could take over a year to build the body using just a trickle of energy from the ZPM but he wanted to make sure the power drainage would be overlooked by all but the most zealous scientist using the deepest scans. He had even stolen a DNA sample from the medical section so the new body would be Elizabeth Weir rather than have Elizabeth look like someone else. Once the body was finished he planned to transfer her consciousness into it, and then she would be just as fragile and vulnerable as any human once more, subject to the same ravages of time as the original Elizabeth.
She would have a chance to live her life afresh, even seek ascension if that was still her wish.
It was the least he could do to make amends for the misjudgement he had made all those years earlier when he reactivated the nanites in Elizabeth to save her life. He winced. Perhaps he had misjudged but he couldn't truly call it a mistake because if he had let her die then Atlantis would have been trapped between the stars with a rapidly shrinking force field and no hope of rescue before the shield collapsed completely exposing them all to the vacuum of space. They had needed her to help them infiltrate Asuras, the Replicator home world, and steal the ZPMs needed to power the star drive and the shield.
What Rodney had not factored in was Atlantis returning to Earth to fight off a Wraith superhive, ending up parked just off the San Francisco coastline on Earth.
The number of scientists in the city had more than quadrupled due to the easy access on Earth, which made it a real headache for Rodney as he was being pulled in different directions constantly, trying to keep people alive because who knew what dangers lurked in the city. The military had sent in dozens of structural engineers to check out the other towers. The engineers were assessing the damage from where the shield had contracted during their flight from Lantea during the Replicator attack, when they lost Elizabeth. Most of the original damage from being submerged beneath the Lantean Ocean for ten thousand years, and from the Wraith attack in their first year on Atlantis, had been repaired by the Asurans while they had temporary control of the city. Rodney still felt sad for the loss of Captain Helia and the crew of the Tria.
Although Atlantis was the size of a small city, from the schedule of repairs Rodney knew it was only a matter of days before someone stumbled across the laboratory and discovered his secret 'Elizabeth' project.
He needed to tell someone; someone he trusted.
That was when he had his first major realization concerning his relationship with Jennifer. He thought he could tell her anything, share all his deepest secrets and desires but when it came down to opening up to her he found it impossible. Rodney knew she would judge him poorly and for all the wrong reasons. He could handle disappointment from her, even anger, but not pity or condescension. She would twist it all to be about her and her needs, emphasizing how he had placed her future in jeopardy, and naively believing telling the I.O.A. or Homeworld Security would be for the best for both of them without consulting him first. He would end up having to tell the I.O.A. eventually but he needed to explore other options first that didn't end up with some pen pusher deciding to terminate the virtual reality and the build of Elizabeth's human body in a knee-jerk reaction, destroying Elizabeth permanently in the process.
Rodney knew there was only one person he could trust to have his best interests at heart, and Elizabeth's, no matter how much it pained him, and that was John. First he needed to man-up and tell Jennifer he couldn't be the man she wanted him to be.
"I'm sorry," he said, choking on the words as he ended one of the best relationships of his life but he knew he could change only so much of his core nature before the stress of trying to be someone else for her tore him apart, and he had a strong feeling his fixation with helping Elizabeth would be that final straw.
Instead of anger or shock he was confused to see guilt and relief clouding her pretty face.
"Rodney, I'm sorry too. I do care for you but being back on Earth... I've been trying to find a way to say goodbye too."
Rodney stared at her for a moment, then sighed as all the recent confusion and discomfort in their relationship gained clarity.
"I guess neither of us has a great track record for knowing how to end.... things." He waved between them and she smiled brightly, making him realize he had not seen her smile since the day Atlantis landed on Earth. She kissed his cheek.
"Take care of yourself, Rodney."
He watched her walk away, feeling regret for just a moment before he turned his attention back to the real problem facing him.
How was he going to explain everything to John without a repeat of those awful, lonely months following the Arcturus disaster?
He waited until their semi-regular 'beer on the pier' that evening, downing two beers in close succession.
"Okay," John drawled, eyeing the second empty can with narrowed eyes, "What's up, Rodney?"
"Nothing," he replied airily. "Just having a drink with my best friend."
"Okay, that's it. I'm cutting you off."
"You can't cut me off just because you think something's up," he exclaimed.
"Rodney?" John growled in warning, and Rodney huffed in annoyance.
"Fine. I split up with Jennifer," he stated, deciding to go with the easy part first
Considering how he had felt after speaking with Jennifer Rodney found it was surprisingly easy to tell John. After just a few short hours he no longer felt any pangs of remorse or regret, which was his second Epiphany that things had not been going so well between him and Jennifer.
"I'm sorry," John replied softly but Rodney could sense the feigned sympathy.
"No... you're not."
John looked at him affronted. "Yes, I am."
Rodney crossed his arms belligerently. "You never liked Jennifer."
"That's not... relevant. You're my friend, Rodney," he wheedled, "And you just broke up with your girlfriend. Of course I feel sorry." John took a swallow of beer....
"I have Elizabeth stashed away in a VR while I build her a human body," Rodney blurted out.
... And John spat out the beer, swiping his mouth with the back of his hand before demanding. "You what?"
Rodney had yet to pick up a third beer, wringing his hands as he faced John.
"I have Elizabeth stashed-."
"Yeah, I heard that. What the hell, Rodney?"
John looked both shocked and angry, which was not surprising under the circumstances. He had been angry when Rodney activated the nanites to save Elizabeth against his orders, and that had lead to her being captured by Oberoth. Yet Rodney could also recall John's sadness when Elizabeth deliberately led the other Replicators to their deaths through the space gate. Over the years they had lost so many people they cared for, or at least felt responsible for: friends, colleagues, scientists, and soldiers.
"It was my... mistake. I wanted to fix it."
"Where is she?" John demanded, voice dangerously soft.
"A laboratory in a tower near the south pier."
By now John was on his feet and Rodney joined him, biting down on the urge to justify his actions and bluster his way through because John was not some pen-pushing bureaucrat. He was Rodney's best friend; a man he would spend a lifetime lecturing in High School Hell in an alternate universe just to give him the time to find a way to bring John home. Rodney doubted he could ever go that far for Elizabeth but he felt he owed her enough to take a chance on giving her back a real life.
"Take me there," John ordered.
Knowing he should be feeling guilty and contrite, Rodney tried to keep the eagerness and smugness out of his voice as he showed John around the laboratory. He led John to where the flesh and blood clone body of an adult Elizabeth Weir was laid out on the cloning table, respectfully covered in a thin sheet from her shoulders to her knees.
"I only need one more week but this tower has drawn some attention. Probably one of those over-zealous scientists noticed the low-level power spikes from-."
"Does she know what you're doing?"
"Elizabeth? Um. Yes. I reprogrammed the VR pod using specifications from the scanners on Atlantis and downloaded her consciousness into it before anyone noticed her presence in the main systems and thought we had another intruder." He took a deep breath and looked imploringly at John. "She's no danger to anyone inside the VR."
"Okay. Can I talk to her."
"Um... Of course." he motioned towards the bank of three VR pods on the other wall that were strikingly similar to the ones they had found on the Aurora.
Rodney helped John into one of the virtual reality pods, and stood back with a soft sigh as the lid closed and John entered Elizabeth's virtual reality. Time moved differently inside the virtual world depending on how much power Rodney diverted towards it. In low power mode a minute inside the virtual world was equivalent to an hour outside, but when Rodney engaged full power mode so he could enter and speak with Elizabeth, a conversation that would take an hour inside took only a minute in the real world. It was these power spikes that were gaining unwanted attention, which was why he had reduced how often he checked in on Elizabeth since arriving on Earth.
Less than two minutes after John entered the virtual reality the system disengaged and the pod lid rose. John sat up and Rodney could tell most of John's anger towards him had vanished leaving just a low simmer of annoyance.
"How is she?" Rodney asked tentatively. "I haven't had time to check on her for a few weeks because of the whole superhive and Earth, and power spikes when accessing-"
"She's fine. She asked me to say thank you for the upload of Jackson's research papers. They've kept her mind busy."
"She says now you've let the cat out the bag, can she see Teyla? I said yes."
"Why would she...?"
"You do realize they were a... thing before..."
"Yeah. You know, a... thing," he emphasized.
Rodney looked at John blankly.
"Together," John clarified, and Rodney stared at John in shock as all the pieces finally fell into place.
"Elizabeth and Teyla? Then all those times they were having," he finger quoted, "leadership meetings' and 'girls night out', they were...?"
John pulled a weird face. "I really don't want to think about it."
"Yeah," Rodney breathed, equally freaked out.
If it had been two unknown, hot women then he might have shown a little macho interest in the girl-on-girl action, but Teyla and Elizabeth were like family. Rodney clamped down on following the lewd thoughts any further. In the meantime John was eyeing him strangely, licking his lower lip thoughtfully, but he was a clam-mouthed as always regarding anything even remotely to do with emotions and relationships making Rodney wonder what else he had talked about with Elizabeth. Rodney had spent hours with Elizabeth in the virtual environment, catching her up on what had happened since her capture on Asuras, and telling her latest gossip. Thinking back she had asked about Teyla often, and Torren, and he might have let slip a few little known facts about himself, such as his crush on the very male Left Wing in his High School's ice hockey team. And he may have talked a little... or maybe a lot about John. He might have been totally oblivious as to why she wanted constant updates on Teyla, but Elizabeth was astute enough to figure out his feelings for John. He pushed the worrying thoughts aside knowing Elizabeth would respect his privacy.
"I told her you and Keller broke up," John added abruptly.
"Oh. Oh, good because..."
Rodney waved his hands, trying to convey how good it was that he didn't have to tell her himself. Elizabeth had not seemed that enthusiastic or happy for him when he mentioned he was dating Jennifer. Instead she had appeared a little... disappointed, and maybe that should have been another Epiphany that he and Jennifer were not going to work out as a couple in the long run. Although Elizabeth hadn't said it out loud she had inferred he was settling for second best, but as the person he truly wanted was unobtainable, second best had seemed more than good enough at the time. He felt a pang of guilt because that had never been fair on Jennifer. She deserved to be someone's first choice, and at least he had fixed that mistake now.
This brought him back full circle to another 'mistake' he had wanted to rectify.
"So... You'll help me?"
"I'll help you divert attention away from here for another week."
"Well, good. That's good."
Although he knew it was a Matriarchal society, Rodney had never really thought too hard about Athosian customs other than the memorial tea ceremony he had performed for Teyla on the anniversary of her mother's death. He believed Teyla had broken with custom when she handed leadership of the Athosians over to Halling but learned Halling was a trusted advisor in her absence, handling the day-to-day leadership of her people. All major decisions concerning the Athosians still had to come to her. In many other cultures she would be known as Queen Teyla. Rodney also knew Kanaan was a childhood friend but now he also wondered if, like him, Teyla had settled for second best when she took Kanaan as her partner, or consort. As he reflected on his decision to move on with Jennifer when the person he truly wanted was rarely more than an arm's length away, he wondered how she would feel on learning Elizabeth was not only alive but soon to be human again.
With all these thoughts chasing around his head, and the knowledge he had gained since, Rodney felt a little awkward when John brought Teyla to the laboratory. He was aware that once more he knew something personal about her that she had not explicitly shared with him.
Teyla looked as if she was keeping a tight rein on her control. "Will you be able to monitor our conversation inside the machine?"
"Yes... unless you want me to switch off that function?" he added cagily.
"Yes, Rodney. I wish to speak with Elizabeth in private."
Rodney keyed in the commands to stop the monitoring process and nodded, watching as she gracefully settled into the virtual reality pod, her expression blanking as the system engaged. She returned almost ten minutes later, the equivalent of three hours spent inside, with her eyes warm and her smile soft with lazy contentment and happiness.
"Thank you, Rodney."
"Am... You're welcome?"
Elizabeth's cloned body was ready a week later and Rodney was not surprised to find both John and Teyla waiting for him in the laboratory when he arrived to initiate the consciousness transfer. Strangely, he wasn't surprised to find Ronon with them, leaning up against the far wall in his customary, menacing fashion, cleaning under his fingernails with a particularly wicked knife. Ronon glared at Rodney, though Rodney couldn't be certain if he was annoyed at him for saving Elizabeth's consciousness or for not letting him in on the secret.
"This is going to cause a very big power spike," Rodney warned.
John sighed. "So you've said, every day for the past week. It's taken of, Rodney."
Rodney winced but he couldn't help but feel anxious. When he had started the clone process a year ago he never expected Atlantis ending up on Earth before the process was completed - or ever, really. With a smaller science team in Pegasus it would have been far easier for him to hide this final power surge without involving anyone else, except possibly Radek. Radek had taken a month's leave to visit his sister and nephews, so Rodney was glad he had asked for John's help in concealing the power spikes. In Rodney's original plan, discussed with Elizabeth at length, he would present the very human Elizabeth Weir as a 'fait accompli', hoping the saying was correct and it was easier to ask forgiveness than it was to get permission, even though he knew it might cost him his position on Atlantis. He hoped it might not come to that and, to be honest, he had left that for Elizabeth to handle as diplomacy and negotiation were her strengths, not his.
Teyla had insisted on visiting with Elizabeth daily so Rodney suspected they had also discussed this reveal and the possible outcomes at length.
Rodney glanced towards Teyla and caught her watching the clone body anxiously.
"Are we ready?" Rodney asked.
"Rodney," John growled, pulling an expression that clearly meant, 'get on with it'.
It took a few moments to input the command sequence, moving between several adjacent consoles.
"Here goes nothing," he breathed, and hit the 'enter' command before stepping back to stand next to John, leaving Teyla standing beside Elizabeth.
He glanced over at John, gaining a small, reassuring smile as the final sequence encoded and the cloning table began to draw the power it needed to transfer Elizabeth from the VR into her new body. On the holographic console hovering over the top of the clone table Rodney could see the progress bar slowly moving forward.
"It's like waiting for a Windows update to install," John remarked.
"Believe me, this is more complex than anything Microsoft could create," Rodney grumbled, anxious and a little excited to see this finally coming to an end, but he got the reference.
When the progress bar reached 100% the power requirement dropped considerably, the laboratory falling silent for the first time in over a year as all the machinery powered down. Rodney waited anxiously as Elizabeth's eyelashes began to flutter. Her eyes opened and she blinked rapidly several times as if clearing her vision. Her movement stopped when Teyla leaned over her and Rodney felt like a voyeur witnessing a very private moment when Elizabeth smiled brightly up at Teyla. He looked away completely when Teyla leaned in and kissed Elizabeth on her lips, her small hands framing Elizabeth's face. Beside him John grimaced but otherwise remained still. Rodney looked back when Elizabeth finally spoke, looking at each of them in turn.
"John, Rodney, Ronon, it's so wonderful to see you all in the flesh again." Her gaze came back to rest on Rodney. "And I have you to thank for this, Rodney. Thank you."
"Yes, well you might not be so grateful once the I.O.A. find out your here."
"We'll cross that bridge when we come to it," Elizabeth stated, and it was so good to hear her true voice inside the city once more.
Teyla interrupted, and Rodney noticed the woven bag in her arms. "In the meantime I have brought clothing, so if you would excuse us?" Teyla raised a meaningful eyebrow.
Rodney joined John and Ronon in beating a hasty retreat, waiting outside until Teyla allowed them back into the laboratory. Rodney was expecting to see Elizabeth dressed in her Atlantis uniform so he was surprised to find her clothed in Athosian attire.
"Elizabeth?" John looked equally confused.
"John, I've had a lot of time to think over the past year. There was a time when all I wanted was to be on Atlantis but the I.O.A. will never agree to handing the city back over to my leadership. I was compromised. I have far more in common with Carson at this moment, and the best I can expect is the same treatment as him. Restricted movement on Earth with no contact allowed with family and friends outside of the Stargate program, or preferably, stationed on another planet, or in another galaxy."
"We can figure a way around this."
"I may not have succeeded in ascending as a Replicator, but I spent weeks in meditation, learning to focus on what was truly important to me." Elizabeth reached out and took Teyla's hand. "I discovered what I wanted was a person rather than a place." She smiled at Teyla. "I thought I could never have this again, and that hurt more than the loss of Atlantis. John, I have no ties left to Earth, except for our friendship," she added, looking at both John and Rodney.
"Elizabeth and I have spoken at great length within the virtual world. Entering the Great City of Athos has been forbidden for many generations, but the Wraith are no longer a major threat to my people. We will be leaving New Athos and returning to our home world, where I believe there is much to re-discover among the ruins."
Elizabeth smiled. "I'll be leaving with Teyla and putting my linguistic skills to good use, helping the Athosians reclaim their heritage."
Rodney raised his hand a fraction. "I don't want to appear... indelicate, but what about Kanaan?"
Teyla smiled. "Kanaan will be pleased. He has much respect for Elizabeth and will welcome her into our family group." Teyla glanced across at Elizabeth. "Perhaps in the fullness of time Elizabeth might also select Kanaan to be the father of her child?" Her gaze slipped sideways, a smile playing about her lips. "Or perhaps Ronon."
"Not a problem," Ronon replied gruffly.
"I think that's a conversation for another day," Elizabeth replied, her cheeks tinged slightly pink. "The important thing is, when Atlantis returns to Pegasus, I'll be leaving with the Athosians."
"And if Atlantis doesn't head back to Pegasus?" John asked.
Elizabeth looked across at Teyla. "Then I'll still be leaving with Teyla."
It was a bloodbath, in the bureaucratic sense. When he saved John after a solar event sent him 48 thousand years into the future there had been no repercussions as Rodney's actions wiped out the entire time line. In Elizabeth's case he had to justify his decision to go against orders even though this course of action had previously been agreed by Woolsey before Elizabeth's replicator companions proved untrustworthy. Woolsey had willingly stepped forward in his defense, which was more than Rodney could have expected from him. However, the fact remained that he had gone behind Woolsey's back, and he had set up countermeasures to avoid detection, proving he knew what he was doing was wrong.
He expected to be relieved of his position as Chief Science Officer on Atlantis, and in that he wasn't disappointed, and yet it still came as a blow. Yet the biggest shock was seeing John take the fall with him.
"Colonel Sheppard, were you aware of Doctor McKay's actions?"
"And did you take steps to bring this to the attention of your superiors?"
Later when Rodney confronted him, John smiled wryly.
"Rodney, it didn't matter if I'd known right from the beginning or ten minutes before you revived Elizabeth. I learned what you were doing and I assisted you, helped you cover up the power spikes rather than take it to Woolsey and I.O.A., or to General O'Neill." He winced. "The truth is... Elizabeth was my friend too, and we'd lost so many good people over the years. I wanted you to save her."
In the meantime Rodney hated to think of how many tests Elizabeth had to go through, both mental and physical, before they were convinced she truly was Elizabeth Weir. Once she was cleared Rodney stepped back in amazement as he watched her and Teyla form a united front. Listening to them he felt a sense of awe. This was the Elizabeth Weir who had negotiated strategic peace treaties between rival factions on Earth, earning herself a place in the Stargate program. This was the Teyla Emmagan who was the leader of the Athosians, and their chief negotiator for trading with other worlds. Together they were a formidable partnership as they began to negotiate for Atlantis to return to Pegasus, strong and impassioned, drawing on all their knowledge, including all Elizabeth had learned on Asuras as a Replicator. He watched them pick apart the opposition, offering trade in knowledge and Ancient technology, plus the protection only Atlantis could provide for Earth and the Milky Way by keeping the Wraith contained in Pegasus. He saw the opposition falling away as each member of the I.O.A. council reached an agreement.
Atlantis would return to Pegasus under civilian rather than military control.
Rodney watched a true master of negotiation work as Elizabeth made it appear a grand sacrifice for stepping down as the civilian leader. He knew she had no intention of returning to her previous position on Atlantis, and was content to hand the reins back to Woolsey, but the I.O.A. did not know that. Somehow, she and Teyla convinced the I.O.A. and homeworld Security that sending John Sheppard back as its military leader, and Rodney as its Chief Science Officer would be a fitting punishment as they would be stationed in an outpost ar from Earth, making it sound like the equivalent of a posting to the outer reaches of Antarctica in John's case, and of Siberia in his.
It was a master stroke, and if anyone on the I.O.A. council realized they had been manipulated so expertly they kept their silence.
Three months and six days after Elizabeth's return John sat in the control chair and closed his eyes. Rodney checked all the monitors, excited and nervous as he felt the stardrive engage, the city vibrattig beneath hsi feet. Atlantis still had a high compliment of engineers and scientists who had chosen to stay on-board. Many of the worst affected areas in the city had been repaired, and several more floors had been opened on the main tower to accommodate the increased numbers.
"Yes, yes, Rodney. Power is at optimum."
Rodney turned and found John watching him, a smile playing about his lips, the same easy smile he had woken up to this morning. Having seen Elizabeth and Teyla team up to take on the I.O.A. together and winning it was little wonder they had also succeeded in getting him and John to finally admit their feelings for each other. So many years wasted believing the other was unobtainable, and Rodney had no intention of wasting any more time.
"John? Let's take our city home."
John's smile widened as he closed his eyes once more to concentrate of the intricate commands required to raise the city from Earth's ocean without causing a tsunami.
Days later they touched back down on Lantea, Atlantis's home world for at least ten thousand years, floating on a different ocean this time. The Flagisallus - Lantean whales - began to circle in greeting but this time they did not stay too long, causing just a few minor headaches. He wondered if Sam was among them.
The day had finally come to say goodbye to Elizabeth and Teyla. Rodney waited beside John and Ronon as the Stargate opened to Athos, humming softly in contentment as Halling welcomed the return of their leader, and of Elizabeth. Around the atrium they were joined by many others from the original expedition as well as later recruits who had known Elizabeth and Teyla for so many years, wanting to wish them well in their new adventure even though they would always be welcome back at any time. Elizabeth had used all her back-pay to buy equipment and items needed by the Athosians for personal use and for trading. She had issued an open invitation to Daniel Jackson to join her in her research on Athos, and Teyla had issued another open invitation to John, Rodney, and Ronon to visit any time, and stay as long as they wanted.
Rodney watched as the equipment was rolled through the Stargate until finally only Elizabeth and Teyla remained. Teyla turned and nodded graciously before stepping through leaving only Elizabeth. It reminded Rodney of that first time in the SGC, when Elizabeth insisted on being the first civilian to cross into Atlantis after it had been deemed safe by the military. He had already said his personal goodbye to both of them but now he watched as her eyes roamed the beautiful atrium with its grand staircase leading up to the control room. She dipped her softly head to him, John, and Ronon, before nodding more firmly, expression setting to quiet joy and determination.
It was time to move on, and she had a whole new life and world ahead of her now.
As Elizabeth turned and walked away Rodney felt John's fingers slide between his own, holding his hand firmly as if promising he would never let him go.