Work Header

Natural Selection

Chapter Text

1.36 hours until system reinstallation

"Finch, I'm going dark."

"Miss Shaw, I really don't think that's-" But the line went dead. "A good idea," Harold mumbled quietly to himself. Although he wasn't entirely surprised by Shaw's decision, he had hoped she would have gone with Reese and Fusco. They were stretched entirely too thin, the odds stacked against them and Harold worried for all of them. Even Root.

Something had changed between Root and Shaw's relationship, even Harold had seen it, although he had pretended not to. He had hoped it would quell Root's more violent tendencies when Shaw woke up from her injuries. But then again, violence never was really solved with violence.

He realised now that perhaps he had been a little too harsh with Shaw in his anger. But she had been an easy target to take out all his guilt on.

Perhaps he should have taken it out on himself.

Because he still questioned his decisions, right from building the Machine to trusting Control. And even now, with Reese and Fusco on their way to stop Samaritan, Harold still wasn't sure he was doing the right thing. All he knew was that he couldn't keep doing this, couldn't keep hiding and living in fear. Samaritan wasn't his creation, it didn't care about people like the Machine had, but if it could watch and listen, could sense the danger and alert the government to threats before they occurred, then Harold would take it. Because even if there were no more irrelevant numbers, at least they could stop the worst of it.

Control had given him the information he needed to access Samaritan's systems remotely, so for now it was just a waiting game until Reese and Fusco reached the site. Harold sat surrounded by computers, his home away from home, his niche, and waited, trying not to let his nerves get the best of him.

Tried not to think about all the mistakes he had made.

"Okay, Finch, we're in," said Reese over the earpiece about an hour later.

"Be careful, Mr Reese," said Harold, a warning that had left his lips on so many other occasions, but never before had Harold felt so intently the need for them.

"Okay, Finch," said Reese a few minutes later. "What am I doing with this thing?"

"Just hook the device up like I showed you," said Harold wishing he was there to do it himself.

"That’s it," said Reese. "You got access yet?"

"Establishing connection now," said Harold, typing eagerly on the keyboards surrounding him as new information rapidly appeared on his screens. Four laptops in total, all set up to confuse Decima's security systems so that Harold could hack his way in and gain access to Samaritan's operating systems.

It was easier than Harold had been expecting, a little too easy, but any concerns he had that this was some kind of trap quickly dissipated as computer code began to flash across all four computer screens.

"Oh my," said Harold. He recognised that code. It was his code.

Harold stared at the computer screens, unable to fully comprehend what he was seeing. Then they all suddenly became blank again, the retinal afterimage the only thing convincing Harold that he hadn't made the whole thing up.

Then the screens began to fill again. The same two words over and over again.

Hello Admin... Hello Admin... Hello Admin... Hello Admin... Hello Admin... Hello Admin... Hello Admin...Hello Admin… Hello Admin... Hello Admin... Hello Admin... Hello Admin... Hello Admin... Hello Admin... Hello Admin...Hello Admin…

"Finch," said Reese over the earpiece. "You’re not going to believe what I'm seeing."

Harold continued to stare at his computer screens for a moment, Reese's voice a faraway echo before he snapped back to reality.

"I think I might," Harold muttered.


0.44 hours until system reinstallation

"You know, as much as I find Shaw to be a pain in the ass," said Fusco, "I’d much rather she was going into this heavily armed fortress with us."

"Relax, Lionel," said Reese. "It's not that heavily armed." But even as he said it, Reese spotted four armed guards out front.

"You want to tell me what that was all about?" said Fusco.

"Nope," said Reese and got out of the car. He didn’t really know what ‘it’ was all about himself and most of him didn’t really want to know anyway. But he knew Shaw would have been useless coming with them if she was constantly worrying about Root. Reese shook his head, not surprised at all that Root had fled the first chance she got. He just wished Shaw hadn’t got caught in the cross fire.

Reese had been watching the guards for the past twenty minutes, assessing their routine, their weakest point. He gestured for Fusco to follow him as he made his way to the side of the building, avoiding the security cameras that Control had warned them about. The entire building was surrounded by a high chain link fence. Fortunately, it wasn't electric, and Reese was able to cut his way through it, a hole big enough for them both to fit through.

"Stay behind me," Reese said quietly, darting to the side of the building and keeping within the shadows. From his recon he knew that one of the guards would be coming this way on his rounds in about thirty seconds. Reese was ready for him and the guard didn't notice him or Fusco when Reese hit him on the back of the head with the butt of his gun.

"Tie him up," said Reese, handing Fusco a couple of zip ties.  He removed the guard’s security jacket and cap, taking the guy’s radio as well for good measure.

"What are we supposed to do with him?" said Fusco, tying the unconscious guard’s hands behind his back.

Reese shrugged. "Hide him in the bushes. Wait here," he added.

Now dressed in security uniform, Reese confidently made his way round the front. Two guards remained at the entrance at all times, with the other two making rounds around the perimeter of the building. Reese walked right past the two stationary guards, keeping his head ducked low as he rounded the other corner without either one of them batting him an eyelid.

"So much for high-end security," Reese muttered to himself.

The third guard was about fifty meters in front of him when Reese rounded the corner and he sped up his pace, grabbing the guard around the throat from behind when he caught up with him. Reese squeezed until the security guard slumped unconscious in his arms and Reese dropped him to the ground with a heavy thump.

Two down, two to go.

The two front guards were still in position when Reese peered around the corner again.

"Hey," he called out, his face hidden in shadow. "Need some help over here."

The two guards immediately rushed towards him, Reese slipping around the corner before either one of them could see his face.

Their eyes immediately fell on the unconscious form on the ground, but before either of them could reach for their radios, Reese shot them both in the kneecaps, his silencer muffling the shots. The two guards dropped to the ground beside their colleague and Reese zip tied all three of them up, keeping them hidden from the security cameras and any other prying eyes that happened to walk this way.

Reese stripped one of the guards of his security uniform and returned to Fusco. "Here, put this on."

Fusco eyed the jacket warily but put it on without argument. "You gonna tell me what this is really about?" he asked as he placed the ill-fitting cap on top of his head.

"Not yet," said Reese. "It's better if you don't know."

"You know that doesn't exactly fill me with great confidence, right?" said Fusco but Reese ignored him.

They entered the building from a side door; Control had provided them with the passcode. Reese didn't like it, and he thought for one moment that it wasn't going to work. That this was all a trap and that Decima would be all over them in seconds. But when Reese punched in the passcode, no alarm bells blared and the door unlocked with a click.

"That was a little easy," muttered Fusco.

"Yes," Reese agreed. This whole thing had been a little too easy, minimal security surrounding the building, blind spots in the security cameras. It felt like a trap.

"Okay, Finch, we're in," said Reese.

"Be careful, Mr Reese."

Reese and Fusco headed down to the sub-basement where, according to Control, the servers were being kept. They met no resistance on the way, the place eerily empty as they walked through the corridors until they reached the security door that led to stairs down to the server room. Reese punched in another security code, and again they got through the door without any alarms going off.

"So that woman," said Fusco, "who gave you all these passcodes - who is she?"

"She works for the government," said Reese.

"Doing what?" Fusco asked.

Reese stopped and stared at him for a moment. "You don't want to know. Here," he added, stopping in front of a power relay box. Reese used a pen knife to prise it open, revealing a mesh of wires and circuitry.

"Okay, Finch," said Reese. "What am I doing with this thing?"

"Just hook the device up like I showed you," said Harold.

Reese did as he was told, taking the small device out of his pocket and hooking it up to the wires in front of him. It was trickier than he had been anticipating and Fusco kept glancing at him worriedly, gesturing for him to hurry it up. Reese worked as fast as he could with the small black device, similar in size and shape to a cell phone and ultimately having the same function. According to Finch, this little plastic box would allow him access to Samaritan's systems.

Reese took his word for it.

"That’s it," said Reese. "You got access yet?"

"Establishing connection now, Mr Reese."

Reese almost said something in reply, but Fusco chose that moment to start gesturing wildly at him. Someone up ahead, he mouthed.

Reese nodded and followed Fusco cautiously up the corridor. The lighting was dim so Reese didn't get a good look at the other person until they were right on top of him.

But Reese recognised the young man as soon as they were close enough, dressed in a white lab coat and fake ID badge to match.

"Don’t shoot," said Reese, lowering his gun and gesturing for Fusco to do the same, as words tumbled out of the young man’s mouth in rapid Japanese.

"Slow down. Daizo, right?" said Reese, recognising the former member of Root's little gang of geeks. "What are you doing here?"

"You know this kid?" said Fusco.

"Sort of," said Reese. The kid look terrified and his English was too patchy for Reese to get a decent answer out of him.

"Don't move," said a voice behind Reese and he felt the hardness of a gun barrel between his shoulder blades.

"Jason Greenfield," said Reese, chancing a glance behind him. He didn't think Greenfield had the stomach to shoot him and judging by the way the hacker's hand was trembling, Reese's instincts were probably right.

"You know these guys?" said Fusco.

"Not exactly," said Reese. To Greenfield he said, "I'm going to assume Daniel Casey is somewhere here too?"

Greenfield nodded. "What are you doing here?"

"Funny," said Reese, but he wasn't laughing, "I was going to ask you the same thing."

Greenfield gestured for them to follow and led them into a large room housing what looked to be a hundred servers. Or at least what Reese presumed to be servers. Daniel Casey was crouched down in front of one, messing with its insides.

"We're almost finished," Greenfield said, lowering his gun now that he had determined Reese and Fusco were not a threat.

"Finished doing what?" asked Reese.

"Honestly," said Greenfield, watching as Casey closed the front of the server and clicked it back into place. "We're not sure."

Reese raised an eyebrow, wondering if this had been part of Control's plan. But he didn't think the ISA had been aware of Root's little band of nerds.

"Two weeks ago, the three of us were each sent one of these," Greenfield explained. He held up a small rectangular black box.

"An external hard drive?" Fusco asked.

Greenfield nodded and handed the hard drive over to Casey so he could place it in one of the other servers. "They all had nothing but computer code on them."

"Code that didn't make sense," Casey added, his voice muffled slightly as his head was currently in a server.

"Not until we put all three together," Greenfield finished.

"Computer code for what?" Fusco asked with a frown, but Reese was starting to get an idea where this was going.

"Some sort of AI system," said Greenfield.

Daizo said something in Japanese. Reese only caught a few of the words and he turned to Greenfield for an explanation.

"He says to tell you about these," said Greenfield, lifting up the ID badge attached to his lab coat. "We got these sent with the hard drives. Started working here the next day under new aliases."

"Someone planned for the three of you to meet here?" Reese guessed. "That code - it’s going to override Samaritan, isn't it?"

Greenfield nodded. "If it works."

"Well," said Casey. "We're about to find out."

Casey closed the last of the servers and they all watched as the columns of blue lights flickered. Around them, all the servers started to hum to life. Reese and Fusco glanced at each other, neither of them sure if that was a good thing or a bad thing.

"It worked!" said Casey sounding as surprised as Daizo and Greenfield looked.

"What worked?" said Fusco.

Reese clicked his earpiece on, suddenly very sure that taking over control of Samaritan was no longer an option. "Finch, you're not going to believe what I'm seeing here..."


0.22 hours until system reinstallation.

Decima's HQ looked like any other nondescript office building, tall high-rise with glass windows and badly functioning air conditioning. Decima Technologies had bought out the entire building, but only two floors of the six hundred foot skyscraper actually housed Decima itself. The other offices were all just a front - empty for most of the time, but occasionally rented out for six months or so, never longer than a year. Nobody stayed long. And nobody knew about the two sub-basement floors housing Decima Technologies.

But Root did.

The Machine had told her, months ago when She was planning contingencies before Samaritan first came online, only ever giving Root just enough information to carry out Her orders, to survive.

So here she was, carrying out the last mission the Machine had given her. To what end, Root did not know. But she trusted the Machine and she would carry out Her last orders even if it was the last thing Root did.

Because that was how the Machine had worked at times; never quite giving Root enough information to hang herself with. The Machine had liked to let Root figure out the bigger picture on her own, and part of Root suspected the Machine was testing her - testing her loyalty and her intelligence.

Decima's front security was pitiful - but then again, Root supposed, who needed security guards when you had a God watching over you? But Samaritan had been shut down for almost two weeks, so she was cautious as she entered the front of the building. One guard sat behind the front desk, a screen of security cameras in front of him. Root walked up to the desk, flashing the guard her most charming smile. It fooled him long enough for her to get her Taser out and shock him until he lost consciousness.

She left the guy breathing and Root didn't know why, if she was doing it for Harold or the Machine. It wasn’t like either of them were watching anymore. But something stilled her hand and she let him live. Because a killer wasn't who she was anymore. She'd still kill when it was necessary, to protect a life or her own. But killing this guard wasn't necessary. So she left him, tied up and unconscious and left to find her real target.

Because killing Greer was necessary.

Getting access to the sub-basement was easy and if she had been thinking straight she would have sensed something was off the minute the elevator doors opened to reveal the offices of Decima's HQ. They were empty bar the lonely figure in the centre office, his back to her.

"Miss Groves," said John Greer, "I've been expecting you."

Root didn't let his calm and arrogant demeanour faze her. This was the second time she had come face to face with this man with a gun in her hand and, like then, she was more than ready to end his life.

Greer turned to face her and, despite the dim lighting in the office, she could see every line on his face, betraying his age.

"If you are here to stop Samaritan," said Greer coldly, "you're too late."

"I like to think I've still got a bit of time left," said Root, although not much longer if she had her timings right. Except that wasn't her mission, and she had to force herself to stick to the Machine's plan, to distract Greer - kill him if necessary - until... until what, she wasn't sure. The Machine hadn't told her that part of the plan.

Greer laughed, but it lacked any humour and he stared at her long and hard as if he could see right through her. "And just what exactly is it, Miss Groves, that you hope to achieve here?" said Greer. "You should have joined me when you had the chance."

"No," said Root, the gun still steady in her hand. "I should have killed you when I had the chance."

"Ah," said Greer, as if it all now suddenly made perfect sense. "Is that what you're here for?"

"I would have thought that were obvious," said Root, waving the gun slightly in his direction.

"And yet," said Greer slowly, "you still haven't shot me. Why is that, I wonder?"

Root didn't have an answer to give. She was wondering the same thing.

"Has Harold Finch's team of little heroes got to you?" Greer asked with a hint of disbelief. "Do you think you're one of them now?"

"Shut up," said Root. Because there was a hint of truth to his words. Harold's team had gotten to her, in more ways than one, and all of them in their own special ways. Harold with his moral guidance, Reese with his fierce loyalty, and Shaw...

Shaw who - on those rare occasions when she wasn't glaring at everything and everyone - looked at her like she cared, like Root mattered.

And that wasn't something Root wasn't used to seeing.

But Root tried not to think about Shaw, how much it hurt just remembering the feel of her. And she didn't like to think about what she had done, how she had left things and how Shaw must have taken it.

She pushed all those thoughts away and focused on Greer.

Because she wasn't one of them and she never could be.

He laughed again and she suddenly felt very afraid - because he wasn't.

"Do they still think you're crazy?" asked Greer.

"I'm not-"

"Yes, they do, don't they?" said Greer. He was taunting her, playing for time. She knew this, yet his words burned her like hot coals.

She cocked the gun, straightened her arm a little but Greer didn't even flinch and she wondered if the dimness of the room was enough to cover up the tremble of her hand, the shine of tears that pricked in her eyes.

Her finger hovered over the trigger, but she couldn't do it. Couldn't squeeze it and end a life.

You’re better than that.

Shaw's words had seemed like a desperate attempt to appease her at the time and Root hadn't known whether to believe them. But she had listened and she had realised that killing some random innocent guy wasn’t going to solve anything.

But killing Greer was something she had to do, it was necessary... And yet she still hadn't done it. The Machine's last orders echoed in her ears... Distract Greer for as long as possible. Kill him if you have to.

It wasn't the first time the Machine had gone against its programming and issued a kill order, but that didn't make it any easier.

Her trembling hand had started to shake violently. She may not be part of Harold's team, may not be one of them, but that didn't mean she had to stop trying.

Root lowered the gun and Greer smiled.

"Samaritan will be born again, and you, my dear..." said Greer, revealing the gun he had hidden behind his back. "You won't be alive long enough to see it."

Root didn't give him the satisfaction of closing her eyes, of hiding from death as if she could escape it.

But gunfire went off before Greer could pull the trigger. He went down hard, his kneecaps suddenly blown to pieces, the gun flying wildly out of his hand.


She looked angry, more than her usual, as she walked up to Greer and kicked him in the face to knock him out.

"How long were you standing there?" Root asked, a little breathlessly. How much did you hear?

"Long enough." Shaw picked up Greer's discarded gun and tucked it in the waistband of her jeans.

"Were you going to shoot me?" Root asked, although she already suspected the answer.

"If I had to," said Shaw. And Root knew that she would have. "Didn't have to," she added,  shrugging nonchalantly.

Shaw was doing a spectacular job of avoiding her eyes. But she came. She came to Root's rescue once again. Root took a step forward, her hand reaching out to the other woman against her will and tried not to flinch when Shaw took a deliberate step back, a cold hard glare directed Root's way.

"Shaw-" Root began, her voice so unlike her own, cracking under the pressure of Shaw's glare.

"We need to go," said Shaw, stepping past her.

"That's it?" said Root. "'We need to go?' Aren't you going to punch me or something?"

Shaw whipped around to face her, like her carefully controlled anger was an elastic band and it had finally snapped under the strain. "Don't tempt me," said Shaw gruffly. "So unless you want to continue your one woman suicide mission, let's go."

"I knew what I was doing," said Root, not moving even as Shaw inched towards the elevator.

"I don't want to hear it," said Shaw.

"The Machine-"

"Stop," Shaw snapped. "Just shut up."

"Why?" said Root, knowing that her words, her incessant need to explain herself, were only fuelling Shaw's anger.

And that's exactly what Root wanted. She knew that if she kept this up, kept taunting her, Shaw would lash out.

"Come on, Sameen," said Root in that sickly sweet way she was so good at. "Hit me."

"You want me to hit you?" said Shaw taking a step forward and Root could see the barely suppressed rage in her eyes. She liked to pretend she could see something akin to hurt in the other woman's eyes too, but Root didn't know if Shaw was even capable of feeling that. Maybe the other night had meant nothing to her, just another passing one night stand in the life of Sameen Shaw. Maybe Shaw was just pissed she'd had to come all the way down here in the middle of the night.

Maybe she never gave a damn after all.

But if Root could make her snap, make Shaw reveal what she was truly feeling in that complex way of hers, then maybe it did mean something after all.

Root stared at the other woman, so close now that Root could reach out and touch her if she wanted to. If Shaw would let her.

Root was crying, she realised, the tears streaming down her face as Shaw continued to glare at her. "I'm sorry," said Root. And she was. For everything. For the Machine. For Shaw and the way she had screwed everything up.

But her apology was the final straw as far as Shaw was concerned.

Root saw the punch coming. Felt Shaw's fist connect with her jaw. Felt the pain radiate outwards. But it was all background noise compared the screeching that started in her left ear, like someone was drilling a hole in her head.

Root cried out and dropped to her knees.


System reinstall initiated…