'Sir, it's finally happened,' the balding scientist says. 'We broke her. We found a simulation in which she will kill Miss Groves.'

'Excellent,' smirks Greer. 'Then we know the location of their safe house, and the Machine.'

'Not quite. Killing Miss Groves triggers a catastrophic failure in the programming. Miss Shaw's brain refuses to comprehend the event, and at that point it completely shuts the simulation down.'

Greer looks down at his vibrating phone, reads the message from Samaritan, and smiles. 'We're running out of time. Run the same simulation again. If it yields the same results then prepare the complex for Miss Shaw's escape. She may be able to shut down the simulation, but if the event occurs in real life she will lead us to the Machine. At the very least she'll take out two of the Machine's Primary Assets.'

Shaw jerks awake, her eyes dilating and breathing heavy. She can feel a thick metal pole pushed against her forehead and the cold hiss of the oxygen mask around her mouth. The room is lively with doctors, nurses and a surgeon.

With the words, 'a little more irrigation please,' she feels the parting pressure of a scalpel behind her ear. 'Soon you'll forget it's even there,' brings a new sensation, something sliding between the skin of the incision. 'You might feel a tiny pinch. Almost done.' With that everything goes dark.

Shaw once again awakens to sound of a man making idle small talk at her. At first she is confused, because all she can see is red triangle blinking under a black line. The man who has been talking at her removes a pair of high-tech glasses from her head, and she can finally see the room she's in. She refuses to move or give any sign that she is conscious, staring blankly ahead into the distance.

She is questioned by a Samaritan operative in an expensive suit with a smarmy British accent. He plays a game with her: 'Dead or Alive,' and though the muddle of drugs keeping her sedated she feels something stirring; a sense of familiarly. The man shows her pictures of Root, Reece and Finch and asks again 'Dead or Alive?' She doesn't know. She doesn't know how long she's been gone. She knows the flutter of panic in her heart after seeing Root's picture will give her away, so she turns to the man and tells him, 'the first thing I'm going to do when I get out of these straps, is make you bleed.' As she is put back to sleep she thinks that even those words sounded strangely familiar in her mouth.

Looking into the mirror of the recovery room Shaw removes the bandage behind her ear and probes the incision mark lightly. Touching it stimulates a sudden burst of euphoria that radiates through her body. In confusion and rage she smashes her chair into the observation mirror, scooping up a piece of shattered glass from the floor as once again she's sedated. When she wakes up the glass is miraculously and surprisingly still clutched in her fist, despite all her muscles relaxing with the sedative.

Once inside an elevator she uses it to cut the restraints holding her in the wheelchair, head-butts the nurse, takes her gun and shoots the smarmy British man in his thigh. She shoots the camera and several men sent to disarm or kill her, then makes her escape. A boat is waiting for her to steal on the shoreline, and as she thinks of how that's just a little bit too convenient, whatever the chip is doing to her brain releases another batch of endorphins.

What Shaw doesn't see once she's left the island is a radio call going around all the men she's shot, who pick themselves up, brush off the dust from their suits, and remove the squibs they were using to make it look like they'd been hit by bullets.

Everything Shaw does from the moment she leaves the island is plagued by that same sense of déjà vu; from taking a taxi into the city, to tying up Bobby and taking out the Samaritan agents sent after her. Then she hears a voice she feels like she's been waiting years to hear. 'Whoever's back there kick over your weapon and I'll let you keep full mobility.' She kicks over her weapon and instantly knows the leg that steps on it.

Root strides around the corner and freezes. She breathes out the word 'Shaw' as though she's been punched in the chest.

'Not a very friendly homecoming,' Shaw jokes, and it's almost like she's never been gone. But looking at Root drinking in the sight of her, it's very clear that she's been gone longer that she anticipated. She stares right back at her, time almost standing still. 'Thanks for saving my ass,' she says sincerely, softer than she intended to.

Whatever she expected Root to say next doesn't come. Root takes a step forwards, reaches out a hand to touch Shaw, and bursts into tears. She sinks to her knees sobbing on the floor and Shaw reaches out to catch her, holding her heavy body tightly to her chest. For the first time since escaping the compound the sense of déjà vu is shattered, this is a completely new experience. Whatever is happening the chip in her brain doesn't like it, and Shaw starts to seize.

A concerned and gruff voice comes into focus. 'Samaritan will be tracking her; we can't take her back to the Machine just yet.'

Shaw feels herself being rocked backwards and forwards by the movement of a travelling vehicle and a hand stroking her hair.

'They got in my head,' she says, alerting John and Root that she's awake.

'You're fine. You're going to be fine. We just need to make sure you're not chipped,' Root says soothingly.

In response Shaw moves her hair behind her ear and shows Root the incision and bump under her skin.

'We have to cut it out,' says John.

'You want me to perform brain surgery on a moving train?' asks Root in an uncharacteristically panicky voice.

'Root you can do this' Shaw says. 'I need it out.'

Root takes out a knife with a shaking hand and heats it up with a lighter to sterilise it. She keeps her hand in Shaw's hair and hesitates before cutting into her.

'Hey, do remember how we first met?' Shaw asks Root. 'You tried to burn me with an iron. Fun right? Maybe you'll like this too.'

'A lot's changed since then,' says Root, looking into Shaw's eyes and summoning her strength. 'OK. Let's do this.'

John carries Shaw into the safe house and places her onto a bed. 'Nice digs,' she croaks.

'Want to move in?' Root asks, trying to joke but sounding exhausted. She sits down gingerly at the end of the bed, keeping a respectful distance away. 'Someone else is excited your back.' With that Bear leaps excitedly onto the bed, tail wagging in barely contained glee.

'Bear, leave her be,' a voice says from the other side of the room.

'Finch.' Shaw says relieved.

'It's good to have you back,' he smiles.

'What about the chip?' Shaw asks.

'Gone. It can't hurt you any more,' says Root, holding the shattered remains of the chip out to her.

'And the Machine?'

'The Machine's still alive and well. We'll take you to see it when you're feeling better.'

'We've got to get to Greer, cut off the dragon's head and the body will die,' Shaw spits out unexpectedly. The words come out feeling rehearsed.

'A well thought-out plan takes time,' says Finch carefully. 'We haven't survived this long by virtue of rash decisions.'

'Yeah 'cause actions aren't really your thing, huh? Did you even look for me?' Shaw says bitterly. She's almost surprised at how vehement the words come out, until that moment she hadn't realised she had any hostility towards him. Almost the second the words come out she's hit by a subtle wave of endorphins that erase any questions from her mind.

'We should go John,' Harold says awkwardly. 'I trust you'll recover well from Miss Groves care.' They leave and Shaw is left alone with Root.

'I hope you didn't miss me too much,' Shaw says offhandedly, trying to control the resentment she feels bubbling up from nowhere.

'I never stopped looking for you,' Root says, her eyes filling with tears. She reaches out a hand to touch Shaw but is brushed off.

'It's kind of chilly in here,' Shaw says. Root takes off her jacket and puts it around Shaw's shoulders.

'You should get under the covers. I'll go get you some more blankets.'

As Root leaves the room Shaw starts to convulse. When she comes to, the sheets are clenched in her hands. She has the strange feeling that she's just missed something important.

She stands up dizzily before she knows she's doing it, walking to find Root and get whatever's happening back on track.

She finds Root placing her gun and some explosives in a locker. 'You know I'm not tired' Shaw says seductively. 'It's hard to imagine both of us making it out in one piece.' Root stares at her, torn between lust and concern. When Root makes no moves towards her Shaw moves aggressively closer, pushing her body into Root's and kissing her violently.

Root hesitates, wanting to fall into the kiss, but pulls away. 'Shaw you've just had brain surgery. You need some time to heal.' Shaw kisses Root's neck, pushing her backwards into the dining table. 'I mean it. I'm not doing this right now,' Root says, pushing Shaw away more forcefully.

'So you don't want me now that I'm damaged goods?' Shaw asks angrily.

'Please,' Root says sarcastically. 'You know as well as I do how much I wanted this. I never thought I'd be the one turning you down. But you've been through a lot. As much as I flirt with you I'm not so sex obsessed that I'm going to take advantage of you. I don't want you doing this for any other reason than that you want to.'

Shaw looks at the floor. 'I don't know what's happening to me.'

'You've been through so much. Just take some time to rest.'

'Will you stay with me?' Shaw asks, hating how vulnerable she sounds.

'Of course.'

'You know I couldn't stand you when we first met.'

'But I wouldn't stop bugging you.' They both smile, and Root leads them back to the bedroom to sleep.

In the darkness Root feels the bed beside her. There is a rapidly cooling space that Shaw's body was just laid in. A strangled shout comes from the bathroom and Root jolts up, running to the door.

'Sameen?' She asks, opening the door without knocking and just missing Shaw closing the drawer under the sink. 'Are you OK?'

'I don't know,' Shaw says, her body covered in an unhealthy sheen of sweat.

'Do you want to sit down and talk about it.'

'What?' asks Shaw confused. 'Aren't you supposed to tell me to come back to bed?'

'What do you mean? If you have a problem we should talk about it now,' Root replies just as confused.

'I've felt weird since I got back. I feel like I've been here before. All day I've had this strange sense of déjà vu. Things I'm saying sound like I've said them before, the situations and people I've met are familiar, my escape seemed way too easy. When I try to think about it every gets blurry. I thought it was the chip but it's been happening without it. I don't know what happening. I-…'

Without her having to say it Root knows that Shaw is afraid. 'Samaritan had you a long time Sameen. They're bound to have done more to you than just give you free healthcare and a fancy computer chip. But they never managed to break you, the Machine is safe because of you. The fact that you're here, alive, is enough for me. We all trust you. It's going to take some time for things to go back to normal, but we're all here for you until then.'

Shaw wants to tell her about waking with a gun and explosives in her hand, with no idea how they got there. She wants to tell her that they're hidden under the sink, but she's ashamed, and as she tries to get the words out another wave of endorphins hit.

'Now is when I tell you to come back to bed. Everything looks brighter in the morning sweetie.'

When Shaw wakes up it's her turn to feel the empty bed beside her.

'Hey baby,' the tentative voice of Root comes from the side of her. 'Don't move a muscle; I'm going to go grab you some breakfast.' When Root leaves the room Shaw runs to the sink, hoping the gun and explosives were a bad dream. She opens the drawer and they're still there. Suddenly an unfamiliar wave of determination and irrational paranoia wash over her. She touches her ear piece to listen to the bug that she's placed on Root's jacket, but hears nothing. She vividly remembers listening to Root's voice through the bug, but as she thinks about it, she can't remember putting a bug there after all. Brushing the confusing thoughts aside, she fills a bag with guns and starts to trail her. Somehow she knows that Root will be meeting with John, and she knows the exact location, even there are plenty of places to get breakfast around the neighbourhood.

When she sees them talking together she barges in. 'So I don't get it. You guys think that I'm a double agent or that I'm a bomb about to detonate?'

'Sameen?' Root says bewilderedly.

'John's a professional dick, but I can't believe that you don't trust me.'

'What do you mean? We haven't said anything like that? How did you know we were here? Did you bug me?' she asks trying to hide her hurt.

'No- I don't- I don't think so. But I know exactly what you were saying,' Shaw says angrily. 'Finch has analysed the chip and it's a placebo. You think it means that there's still something wrong with me even without the chip. You think I'm behaving strangely. John thinks I've turned. He wants you to keep surveillance on me.'

'Harold hasn't been able to analyse the chip. We crushed after we took it out of you, remember?' John asks, more delicately that Shaw would have expected.

'And we weren't saying anything about not trusting you. We wanted to keep you out of normal operations until you were healed. Sameen is this like last night?'

'I was fine. I was fine and then all of a sudden I was really angry. I thought I'd bugged you but I knew I hadn't. I knew that you'd both be here. You were supposed to be talking about me.'

John and Root exchange a meaningful look.

'You have no memory what happened while Samaritan had you,' Root says gently. 'I'm almost certain that they will have tried to condition you against us. If you're right about the chip being a placebo then it's going to take some time to get the endorphins out of your system. We just need to lay low until then. Everything will be fine.'

Shaw nods. It doesn't answer all of her questions but it makes sense.

'We should go,' says John. 'It's not safe for you to be out on the streets without a cover identity.'

Shaw follows Root and John to the exit, but as she's about to leave a violent string of images flash though her head. She grabs the phone at the table nearest her and speed dials the first number in there. Before they can grab it off her she says 'this is Sameen Shaw, I know you're looking for me, so come and get me.'

Coming back to her senses she sees the look of shock and panic on Root and Reece's faces. She instantly drops the phone. 'I didn't mean to. I don't know why I did that.'

'What next,' John asks Root hurriedly.

Shaw unzips the bag at her side, surprising herself with the contents; it's full of guns. 'I don't remember bringing these.'

'Samaritan must have wanted you to do that, which means they've given you a plan to follow. Think Sameen, what's supposed to happen next?'

Shaw squints. Somewhere in her mind she knows what's about to happen, but it's like trying to recall a forgotten dream. She looks at Root's face and suddenly it clicks. 'There are agents coming. I'm supposed to lead them into the back room. You knock them out and triangulate the signal of their last call.'

'Then we do the opposite' says Root. 'We leave now and take the blind spots back to the safe house.'

'There's something I'm forgetting,' Shaw says angrily at herself. 'Something important.'

'No time,' says John, 'we can think about it later.'

The three narrowly make it out the back entrance just as two of Samaritan's men walk through the door.

In the alley behind the diner Shaw yells 'GREER. If we'd have taken out those men they would have led us right to him. We could have killed the son of a bitch.'

'Or that could have been a trick to lure us out,' says John. 'Shaw, we can't trust anything that Samaritan's planted in your mind.'

'This could be out biggest chance to get rid of him,' says Root. 'Someone needs to check. I'll go, John you get her back to the safe house.' Root disappears quickly down the street before anyone has a chance to argue.

'We need to get to the Machine.' Shaw tells John. 'This way,' she gestures to an adjoining alley.

'We're meeting Root at the safe house remember? We're not going to the Machine,' John says brusquely.

'What? You got something to say you better nut up and say it.'

'Sameen, you're not yourself right now. That's the chip talking.'

Another round of images rush though Shaw's head and for a moment everything goes black. She's brought back to her senses by the sound of a gunshot. When she looks down at her hands she's shocked to see that she's holding a gun. She looks at John face down on the floor. She sees blood, but she looks away quickly, unable to comprehend what she's done.

Finch has heard the shot. 'John? Sameen? Are you alright?' he asks frantically though her earpiece.

'I don't know what happened. A Samaritan operative came out of nowhere. They got him. John's dead,' Shaw says, feeling the words come out but unable to stop them.

'No, this can't happen.'

'Shaw you have to get out of there. I'll come find you, bring you back.' Root says, a suppressed sob in her voice. I'm coming to get you. I am not ready to lose you again Sameen. Whatever happened, we'll fix it. Just stay alive.'

Shaw feels a hand pulling her gently away from the crowded side-walk she's stepped onto. She knows that the cameras on the street will have alerted Samaritan to her location. Now she needs to lead them to the Machine's location.

'I think we lost them,' says Root. 'The safe house is too far away, we've got to get back to the Machine instead.'

There is a single flash of light in Shaw's mind; something about going to the Machine suddenly feels wrong. 'We need to be sure that we're not being followed first.' Shaw says. Another sharp flash. 'There's something I need to tell you. About Reece.'

'It can wait until we're home safe,' Root says, looking around the street to make sure they're not being followed and blocking Reece's name from her mind until she has time to grieve.

There's another jab in Shaw's mind and this time she can almost make out a picture. Her hand absent-minded touches her gun. 'Follow me,' she says.

A few minutes later they arrive in a park. When they get into the centre of it Shaw takes the gun out of her holster and points it at Root. 'I can't do this any more. I don't know who's controlling this.'

Shaw's body convulses as the bright violent lights in her head form pictures, then memories. She sees this moment a thousand times, she knows that when her eyes open she'll see Root's beautiful eyes filled with tears, as she stares down the barrel of Shaw's gun. She knows exactly where this will end; she's been forced to relive it over and over again for months.

Root steps forward to help Shaw as she seizes, but as quickly as the fit starts it stops.

'I shot Reece,' says Shaw, and Root freezes in her tracks. Shaw raises the gun back up, aiming it again at Root's head. 'I've killed him thousands of times, and now I have to kill you too.'

'What's happening?' asks Root in shock.

'I remember. I remember what Samaritan did to me. This is a simulation. They made me go through this over and over again, trying to get me to lead them to the Machine. But it always ends here, with you. I told you I couldn't escape it. But when things got to be too bad, there was one place I'd go to in my mind. Here. With you. You were my safe place.'

Tears start to roll down Root's face. 'I'm so sorry sweetie. But you're out. We can fix this.'

'There is no out; I'm still in the simulation. I remember the simulation before this one. It was the first time I shot you, and now they're going to make do it again. But you're not real,' Shaw says, looking at Root sadly. 'You're not my Root, you're pieces of code. You're Samaritan in disguise and I can put an end to this.' She flicks the safety of the gun off, ready to shoot.

'That's not true,' says Root urgently. 'Just listen to me for a minute. If Samaritan were able to simulate this it would be flawed. It can only create what it sees, and it can only be influenced by your perception of the world.'

'Then prove it,' says Shaw untrustingly.

'You said yourself that things have been happening differently. At the safe house you thought I'd immediately sleep with you because I flirt a lot, and that's what you expect from me. But I didn't, because we'd just sliced into your brain and I wanted to give you some time to heal. At the diner you thought John wouldn't trust you because Samaritan sees him as a cold rational killer. You were angry at Harold because Samaritan wanted you to be. You need to hold on to these moments when the déjà vu is shattered. You're back with us in the real world.'

'Samaritan could have added all of that to the simulation when previous things didn't work. You need to tell me something I don't know, something that Samaritan can't fake.'

Root thinks for a moment. 'I love you,' she says sadly.

'I already knew that.' Shaw says desolately. She hits the gun against her head in frustration. 'It has to be something I don't know.'

'You love me too,' replies Root. To this Shaw laughs, but without any conviction. 'Don't try and tell me it isn't true,' Root persists. 'Samaritan couldn't know that because it will never understand emotion. It thinks you're a sociopath, and so do you. But I know you Shaw, better than you know yourself. You care about us, you care about the Machine… you care about me. You've proved that over and over again and now you just need to believe it. I'm not asking you to change, but I do want a chance. I don't want us to only kiss when one of us is about to die. I don't want our feelings to only come out when there's a gun pointed at us, or a bomb under out feet. I want to make this real. That's what Samaritan could never know, because it knows nothing about us.'

Shaw looks at Root, her heart beating fast and her breathing ragged. She can feel the sweat between her hand and the gun. She wants to lower it, but can't. She feels her finger slowly, methodically, squeeze the trigger.

The gun recoils in her hands but she keeps pulling the trigger until the clip is empty. The sound is deafening.

Root looks at Shaw in shock, then to the roundabout a few feet away from her which has taken the brunt of all the bullets. After she gets over the shock she says 'you really wanted that thing dead huh?'

'I came so close,' Shaw says numbly. 'I almost killed you.'

'Shhh. It's alright' Root says, stepping forward quickly and taking the still outstretched gun in Shaw's hands from her. 'You didn't, and that's definitely what counts. The playground will be fine.'

'John,' Shaw says, her whole body slumping. 'I killed John.'

'You're going to have to do better than that to kill me Shaw,' a familiar voice says from her earpiece. 'You shot me right through the shoulder. If I didn't know any better I'd think you were a terrible shot, either that or you're going soft on me.'

'Thank God,' says Shaw, sinking to her knees on the ground. 'Root' she says gruffly 'I know you said you didn't want us to kiss again because of a near death experience, but I'm going to need you to make an exception.'

'Gladly,' Root says, taking Shaw's face in her hands and kissing her gently.

Despite her shaking, tired body, Shaw finds herself smiling into the kiss. For the first time since she's come home she feels grounded.

'Ugh, when you two are done I could use a little help,' John says with annoyance. 'This is all well and good but you left me bleeding in an alleyway.'

'We'll be right there John,' Root says, reluctantly pulling away from the kiss.

'Then we need to get back to the safe house,' Shaw says. You need to keep me there, away from the Machine, and any weapons, until the chip is out of my system.'

'I'm more than happy to keep you under house arrest,' Root says flirtatiously.

'That's the Root I remember.'

'Do you still hate it?'

'Not in the least.'

Thanks so much to everyone who's read this. I just updated it because I realised it was saved and published without line breaks, which must have made the jumping around really terrible to read, so my apologies. If you enjoyed this it would be wonderful to hear your feedback, it does my soul good! Thanks, Reanne.