When Sheppard got a call that night from Dr Keller, his sense of foreboding received a frightening boost.

'Colonel Sheppard, I need to see you in the infirmary right away. There's been a development with Elizabeth's nanites.'

Having not yet settled into bed, he leapt up and sprinted down the quiet corridors, almost flooring Zelenka as he passed him on his way out of the transporter heading to his own room, and arrived in the infirmary in record time.

Dr Keller blinked in disbelief as she saw him panting before her, obviously shocked that he had covered the distance from his quarters to her office in so little time. 'Colonel! I know I asked you to come right away, but I didn't mean for you to give yourself a coronary!'

'The nanites...what's...going on?' he panted, leaning on her workstation and battling to regain his breath.

Clearly realising he didn't intend to indulge in small talk, Keller caught him by the elbow and guided him toward a laptop. On the screen he saw what he presumed was the latest scan of Elizabeth's body. He could clearly see the nanites had replicated and moved to several different areas of her body.

'Oh, God. They're spreading.'

'I don't want you to panic at this point, Colonel,' Keller said firmly, asserting herself before he could start planning their next move. 'The nanites have replicated, but are now holding static again. If you look at where they are located – the thymus, spleen, lymph system, and in her bone marrow – it seems clear they are attaching themselves to the main components of her immune system.'

'Is this because of the virus she's fighting?'

'Quite possibly, but I'm worried something else could be going on.'

Sheppard's heart plummeted and he wondered at which point Keller would tell him something that justified her instruction for him not to panic. 'What?'

'I suspect the nanites are fighting something more serious than a cold. I think her body is trying to reject them. As I said before, they're a foreign object within her, and I'm thinking Rodney didn't have time to work out a way to fool her immune system into thinking they were compatible with her DNA. I think her body is fighting them, and the nanites are spreading out to suppress her immune system. I recommend putting her on a Rapamune protocol to stop the reaction –'

'No,' Sheppard stated firmly, cutting Keller off in mid explanation.

'No?' she repeated, he face reflecting the obvious confusion his order caused. 'But if I don't she could reject the nanites and she'll die.'

'When the nanites first invaded her body, Dr Beckett said they were attacking her immune system in an attempt to take over. How do we know they're not doing the same thing right now?'

'Because they've been reprogrammed. It's not within their capabilities to start attacking her that way.'

'I don't care. Do not administer anything that suppresses her immune system. If those nanites are working correctly, nothing her body can throw at them should do any harm.'

'But I don't know if I'm happy taking the risk...'

'Fine. If you won't take my advice, let me get someone here who can explain things a little better.' He tapped his earpiece. 'McKay. This is Sheppard.'

Nothing.

'McKay, respond.'

'Yes...yes...all right. There's no need to yell.'

Sheppard rolled his eyes and counted to ten in his head in his head. 'Rodney, I need you to come down the infirmary and look at something Dr Keller found.'

'What? Are you kidding? I just got to sleep for crying out loud!'

'McKay,' the colonel growled in warning.

'All right...all right. Just gimme a few minutes.'

Sheppard took a deep breath to calm himself, then asked Keller, 'Have you mentioned what you've found to Elizabeth?'

'No. Not yet ,' the young doctor admitted, chewing nervously at the inside of her mouth. 'I didn't know how much you would want me to say to her.'

'I'll do it,' he grumbled, glad to have the excuse not to look at the woman a moment longer. Much as he'd tried to fight his desire to blame her for the nanites, he was finding it very hard not to, and her continual insistence the nanites were a beneficial presence only served to make him progressively more prone to disliking her. Why could no one else fully understand the danger they were in?

One of the guards outside the isolation room opened the door when he reached it, but he was too focused on the news he had to deliver to even acknowledge them. Inside, Elizabeth was fast asleep in her bed, lying on her side and breathing gently – peaceful, at least for the moment. How could he disturb her with something like this? Perhaps it could wait until morning.

He was about to leave when she stirred, her eyes cracking open just a fraction, and then widening immediately when they fell on him. 'John!' She sat up, almost smiling, but the attempt fell flat when she took in his expression. 'What's happening?'

'I've just spoken with Dr Keller. Your nanites are...behaving outside of their programming.'

Her jaw dropped a fraction, her face blanching. 'What...what does that mean?' she asked, smoothing down her hair as if the very act of making herself more presentable asserted some kind of control over the situation.

'They're invading your immune system. Keller thinks it may be because your body is trying to reject them, but she can't be sure.'

She nodded, maintaining a dignified composure as she looked at him. 'What does she want to do?'

'She wants to suppress your immune system in case the nanites begin to...come loose.'

'And what do you want to do?'

He battled the urge to yell, I want her to stop interfering with you, and said calmly, 'I want her to let your body do whatever it needs to do.'

She nodded again, chewing pensively on her bottom lip. 'The first time the nanites took over, Carson told me –'

'I know...that's why I think we should let your immune system do its thing. Suppressing it will just give the nanites free range through your body.'

The room was painfully silent except for the buzz of the electronic equipment accompanying them. Sheppard tried to think of something else to say, something that would make this all seem somehow less ominous, but nothing came to mind. He was scared for her, and for Atlantis, and he was pretty sure she knew that.

'Do I have a say in what happens to me?' she asked, taking him by surprise, although the more he thought about it, the more logical the question was. This was her life, and if she was suffering from any other condition, they would be asking her what she wanted them to do. But since she had nanites in her brain...

'I doubt the IOA would agree to you making a decision on this,' he said flatly, trying not to show the emotions the thought evoked in him. 'The nanites may mean your judgement is...impaired.'

She took a deep breath in through her nose, then blew it out before saying, 'I see.'

'I know that must sound harsh, Elizabeth, but you have to see it from their point of view. Those nanites in your brain mean you're compromised...they could take over and we might not even know.'

'Who's to say they haven't already?' she asked, her eyes looking moist in the dim light. 'If they're already acting outside of their programming, how can you be sure this is really me you're talking to? You could be endangering yourself even being here.'

He shrugged, feeling awkward that she would fire a question like that at him. It was a case of shooting the messenger, but his shoulders were broad; he could take her anger on board. She sure as hell deserved the chance to vent at someone.

'I wish you could just bring in an EM generator and end all this,' she said more quietly, bowing her head. 'This isn't living – it's barely even existing.'

'That's not an acceptable option, Elizabeth. I wish we could get this sorted out quicker, too, but it's complicated.'

'You think I don't know that?' she snapped. Then, she stroked her fingers across her forehead, took a moment to gather herself, and offered him an apology. 'I'm sorry, John. It's not fair to take this out on you. You didn't want any of this to happen.'

'No one wanted this to happen,' he corrected.

'No. I know. It's just that I was hoping to get out of here soon. Teyla said Dr Keller was considering removing my isolation status because the nanites were showing no unusual activity. I guess this has blown any chance of that now.'

Though annoyed Teyla had told Elizabeth that before knowing it was definite, Sheppard supposed he understood the Athosian's keenness to give their friend some good news. What annoyed him even more was the fact Keller had discussed the prospect with Teyla before mentioning it to him. He wondered if he was being over sensitive because of the insecurity his new position awoke in him, or perhaps, worse still, he was becoming a control freak. But he felt certain decisions like that should be run past him before being discussed with less senior members of the team, and Elizabeth herself would have expected nothing less when she was Atlantis' leader.

Pushing his feelings aside, he replied, 'Maybe it's postponed for a while, but we'll get there.'

Now she smirked, shaking her head. 'You're a terrible liar, John Sheppard.'

'I'm not lying. If McKay can figure out exactly what those things inside you are doing, and it turns out to be non-threatening, you might be allowed out and about yet.'

She sighed, settling back against her pillows with a kind of sad resignation. 'No offence, but I won't hold my breath on that.'

'We're doing everything we can to sort this out,' he assured her, his words sounding hollow even to him. The Replicator technology was changing even as they thought they were getting to grips with it; in truth, he doubted they were going to get a handle on it anytime soon. But he could be wrong about that. Hopefully, by the time he got back to the infirmary McKay would be there and they could figure this out without having to make the kind of assumptions Keller had been jumping to.

'I know you are,' Elizabeth replied quietly, pulling her sheets up over her chest. 'I think I'd like to sleep again now.'

'Sure...you get some rest and we'll talk some more in the morning.'

He headed for the door, but the sound of Elizabeth calling his named stopped him just before he opened it. 'Next time you come in here, you'd better be wearing a hazmat suit.'

Though he didn't want to do it, he realised she was probably right. He nodded and headed back to the infirmary.

Before he reached Keller, he could hear Rodney's frantic tones scraping down the corridor. 'No, no, no, no, no. I don't care what her immune system is doing, the nanites shouldn't be reacting in this way. Why didn't you tell me about this sooner?'

'Because I've only just found it myself. I told Colonel Sheppard and then he called you. We couldn't have moved any quicker on this.'

The colonel strode in, seeing McKay's puce complexion and bulging eyes. 'This is bad, Sheppard. They're adapting. They shouldn't be able to do that.'

'Well, since saving her life is what they're created to do it's not exactly a surprise, Rodney. What I need to know is are they suppressing Elizabeth's immune system to save the repairs they've done, or to strengthen their hold?'

Rodney flicked his eyes down to the laptop and keyed in a few commands before throwing his hands up in despair. 'There's no way of knowing which cause is driving them at this point.'

'D'you think you can bring them back under control?'

'Well, if I continue to write the program you've asked me to create, that would do it anyway.'

'Would it? Can you be certain of that?' Sheppard demanded, fixing him with a hare stare. 'Or is it possible these things are now beyond your control and we need to act to neutralise them?'

'Neutralise them? You mean, shut them down?' Keller asked, her eyes threatening to pop with shock. 'But that'll kill her.'

'And if the Replicator nanites inside her are acting on Oberoth's programming now, they won't hesitate to do the same to us,' he pointed out.

'You think he reprogrammed them, don't you?' Rodney breathed, his eyes darting about as he thought about everything that had happened since her return. 'You suspected this all along.'

'She's in isolation, and everyone has been warned not to touch her. Whatever I thought, I've made sure those nanites don't jump ship, so we shouldn't need to panic, right?'

'Well, I've been monitoring them on a regular basis, so this change has only just happened in the last half hour,' Keller assured him. 'And Elizabeth herself is exhibiting no unusual behaviour or severe adverse reactions. Don't you think shutting them down might be a little premature?'

'Actually, right now, I'm hoping it isn't too little too late. You're absolutely sure no one in your team has come in contact with her?'

Keller shook her head. 'We've all been wearing hazmat suits, so there's definitely been no direct contact. I made sure very member of my team understood the potential danger. No one else has touched her.'

Sheppard nodded. 'Okay. So chances are no one else could have been contaminated even if it's possible,' he said, almost to himself. 'And like you said, there has to be a conscious decision to pass on the nanites, and there's no way Elizabeth would do that.'

'That would seem to be the case,' she agreed.

'Plus the nanites aren't replicating exponentially,' Rodney added. 'They've only created enough new units to go to work on her immune system while the others hold her injuries together.'

'So...non-threatening at this point?' Sheppard clarified.

'I'd say so, yes,' McKay nodded, but he couldn't look him straight in the eye.

Sheppard chewed his lip, giving it some thought. He didn't want to pull the plug on Elizabeth unless he had to; those nanites were her life-support system after all. But he'd given Shen his promise that he wouldn't hesitate if she posed a threat to Atlantis. He had to make a judgement call. 'All right. I'll report the change to the IOA, but recommend that, since there appears to be not threat to anyone other than Elizabeth herself at this point, we continue with the process of monitoring her for the time being,' he announced. 'Rodney, walk with me.'

They left a stunned Dr Keller behind them. Clearly, she'd thought she was going to have to fight harder to save her patient. Once again, Sheppard found himself wondering if he would have made the same decision had it not been Elizabeth in that isolation room. He figured both he and Rodney were allowing their guilt to colour their decisions more than they should, and he promised himself this was absolutely the last time he would do that.

'You think we're going to lose her, don't you?' Rodney asked quietly once they were away from the infirmary.

'I hope not,' Sheppard breathed. 'But if we don't get on top of it soon, I'm afraid those things are gonna run riot again.'

'I should get down to the lab and work on them. Damn it! I should have got a new sample before I left the infirmary!'

He started to turn, but Sheppard caught hold of him and turned him back round. 'You need to get some sleep, McKay. You can't keep functioning on caffeine alone.'

'But time could be of the essence...'

'And you'll probably work faster with at least a few hours sleep under your belt.'

His shoulders dropping, Rodney admitted defeat. 'Yeah, I guess you're right.'

'Considering what's happened, I'm going to recommend we suspend all off world travel.'

Rodney's eyes widened. 'D'you really think that's necessary?'

Sheppard shrugged. 'I don't know, Rodney. But until we get a handle on exactly what's happening with those nanites, I don't think we should be sending anyone else through the gate.'

'Yes...yes...you're right. It would be irresponsible of us to travel to other planets until we have this fully under control. Which is why I should probably get to the lab...' He tried to turn again, but Sheppard caught his arm and dragged him along with him.

'No, that's why you should rest and come at the problem with a clear head. C'mon, I'll walk you to your room...just to make sure you don't change your mind en-route,' Sheppard suggested as they set off again.

The corridors were quiet, with only one or two personnel still active as the end of their shift approached.

Once they were alone, Sheppard asked. 'How's finding a new frequency for the Replicator disrupter coming along?'

Rodney shrugged. 'It's still in the hands of the program. It could take hours; it could take weeks or months.'

'Then I guess we'd better hope it's sooner rather than later,' Sheppard said, trying not to think of the implications of the latter timescale. 'What about the jumper? You got that up and running on remote orders from the chair.'

'The jumper's ready, and the repairs to the chair are almost complete, so it'll be back on-line tomorrow.'

'Well, that's something,' Sheppard said, feeling a sense of relief that they would at least have some defence against external attack. 'And the shields?'

'Hopefully extending across the whole city some time tomorrow, too.'

'That's good, Rodney. We'll be able to cloak, send out a decoy jumper, and defend ourselves if necessary. You should be proud of the work you and your team have done.'

Rodney stopped and eyed him dubiously, shaking his head. 'They really have to get someone else in charge here soon because this supportiveness is really beginning to weird me out.'

'You and me both,' Sheppard admitted, sputtering out a laugh. 'I'm not sure how much longer I can keep this up.'

They reached Rodney's room and the scientist activated the door. 'Well, at the risk of sounding like a cliché – call me...if anything happens, that is.'

Sheppard nodded, awkwardly clapping his hand on his friend's shoulder. 'Don't worry, Rodney. If anything changes, you'll be the first person I call.'

McKay gave him an anxious smile, then headed into his room. Sheppard decided that once he'd fed back to the IOA, and acted on whatever instructions they gave him, he would turn in himself...again. He wondered how much sleep he would actually get tonight, and what his nightmares would tell him this time.