Sheppard lay in his bed and stared up at the dark ceiling, imaginary shadows swelling and retracting as his tired eyes tried to pull details into focus.

He'd visited Elizabeth just before 22:00 hours, just as he'd promised, finding her still looking as fresh as she had that morning when he'd interviewed her. Those nanites kept her going when any average human would flag, and he found the fact they did so hugely disconcerting. They'd spoken for around ten minutes about nothing of any consequence – the weather, surfing, dogs and other such trivialities – always skirting the subject touched on that morning, but he'd sensed she was already growing tired of being cooped up in the same room all day. He could hardly blame her, but until the IOA gave the go ahead for them to remove the isolation protocols, they had no choice but to keep her there. Not that he minded the delay; he felt they needed more time to make a full risk assessment before releasing her into the city.

He closed his eyes, pressing the heels of his hands into them and muttering, 'Switch off, John. Get some sleep!'

Of course, the more conscious of the fact he still wasn't asleep he became, the less likely it was he would relax enough to go to sleep. He huffed out a sigh and threw himself onto his side, screwing his eyes shut and refusing to check the time again. The time was irrelevant; only the fact he was still awake mattered.

A gentle, electronic chime announced someone at his door. He lifted his head and stared at it for a moment or two without moving, wondering who could be bothering him at this later hour. If it was something urgent, he would have had a message via his earpiece rather than someone coming to visit him. The chime repeated and, realising whoever was out there wasn't about to go away, he cast his sheets aside and trudged over to the door to unlock it.

When it drew back to reveal Elizabeth smiling at him, his breath caught in his throat and he couldn't speak.

'Hey, you. Did I wake you?' she asked, peering past him at his dishevelled bedclothes.

'Er...no...no...not really,' he said, raking his fingers back through his hair. 'I haven't got to sleep yet.'

'Well, I just wanted you to let you know in person that the IOA have decided I haven't been compromised in any way during my time with the Asurans, so I'm free to retake my position as Leader of the Atlantis Expedition.'

His jaw dropped at the news, and he mentally groped about for an appropriate response that wouldn't cause her offence. 'Really? That's great. But I'm surprised they didn't tell me themselves considering they asked me to fill your boots for a while.'

'Oh, don't be like that, John. I thought you'd be pleased for me,' she pouted in a manner far too flippant for the situation as far as he was concerned. 'Besides, you didn't really expect any courtesy from them, did you?'

He supposed he didn't, judging by their past record, but that didn't make it right. 'I am pleased for you, Elizabeth. I just think they should've spoken to me about it. Who did they report back to?'

'Does that matter?' she asked, blinking her long lashes at him innocently as she held his gaze.

'It matters to me, yes,' he replied, pushing past her. 'I think I might just contact the SGC and find out why I was bypassed.'

He felt her hand land on his shoulder before he could get more than a couple of paces. 'There's no need for that, John. Everything is just as it should be now. Accept it and things will be much easier for you.'

'What are you talking abou –?' He gasped as her fingers dug into his shoulder, pressure forcing him down to his knees. With one hand, she'd rendered him immobile; he could literally feel his bones crushing under her grip.

'I have control here now, and soon my Asuran brothers will join us and destroy this last great symbol of Lantean civilisation. I wanted you to be here to see it, but if I can't trust you to hold your peace...'

'I won't...let you...destroy...this place,' he grunted, panting against the pain. 'I will...stop...you.'

He reached for his sidearm, but she kicked it away before he could even level it at her. Not that it would have slowed her for long; he'd only intended to use it to distract her while he got free and called for reinforcements. She released his shoulder, but only long enough to circle him and swing a right that knocked him straight on his backside. The bitter tang of blood hit his tongue and stars dotted his vision. It felt like she'd hit him with a baseball bat.

Spitting out the taste of it, he pushed back from her with his feet, too stunned by the blow to stand. She tracked him, smirking as she finally planted her booted foot on his chest and pushed him flat to the floor. 'I'm sorry, John, I really am, but I can't have you running around Atlantis telling people what we're up to. Still, maybe I don't have to kill you. Maybe, if I have a little feel around in that head of yours I can help you to forget.'

'No!' he yelled, trying to force her foot off him, but she was too strong. She bent forward, crushing the air out of him, extending her hand toward his forehead and pushing it in excruciatingly slowly as he screamed for her to stop...

Sheppard fell out of bed, still flailing at an arm that didn't really exist. Hitting the floor woke him with a start, but it still took him several more seconds to realise he was safe in his room and not in Elizabeth's clutches. He gasped in much needed air, and once his heartbeat slowed to a pace that didn't suggest he might arrest, he untangled himself from his bedclothes and half-staggered, half-crawled, into his bathroom.

Absently rubbing at his sore backside, he ran a sink of water to freshen up before realising he didn't even know what time it was. He checked his watch. 0502 hours. That was the longest he'd slept in days, though he didn't feel any better than he had when he'd gone to bed. Soaping up his chin, he shaved, then jumped into the shower to wash away the sticky feeling coating his skin. That done, he dressed and heading out to start the day.

He thought about going straight to the mess hall to grab an early breakfast, but then reconsidered. His dream had left him a little unnerved and there were other more important issues on his mind than food. He had a few things he wanted to check out, so he turned around and headed for the labs, hoping to find someone he could put his questions to. It wasn't exactly a surprise when he got there and found Rodney already hard at work.

'Morning, Rodney,' he called as he approached, forcing on a smile.

'You're up early,' Rodney muttered, as he finished what he was doing.

'Not as early as you, apparently.'

Rodney looked up now to face him. 'God, Sheppard. You look terrible.'

'Thanks for that,' Sheppard grunted, leaning on Rodney's workstation and planting his free hand on his hip as he glared at him.

'Yeah, well...I say what I see, you should know that by now,' the scientist said by way of an apology. 'Anyway, what are you doing here?'

'Thought I'd come for an update.'

'At 05:20 am?'

'I'm awake, you're awake. What's the problem?' Sheppard asked.

'Nothing,' Rodney replied with a sigh, calling up the file containing the latest reports from their repair teams. 'Okay, well, we've been concentrating on repairing the power relays first. We think we may well have them fully functioning before the end of today which means we should be able to extend the shield to cover the entire city.'

'That's good news.'

'Yes, it is. Unfortunately, since the hyperdrive is still off-line, should the Replicators locate us and send another of their satellites, it won't be able to protect us for long. They could soon drain the ZPM and leave us vulnerable again.'

'I'm really starting to hate that word,' Sheppard grumbled, rubbing his jaw.

'Yeah, you and me both.'

'So how about the hyperdrive?'

Rodney called up another file and quickly studied the contents. 'Well, apparently the hyperdrive sustained extensive damage during the flight and landing, and we have to improvise a few new circuits to replace some that are completely shot. That's going to take a few more days, hence the need for the shield.'

'Okay...well...we'll just have to hope the Replicators don't turn up until we can get the city mobile.'

'Yeah. Like I said before, our luck has to change soon, right?'

'Right,' Sheppard agreed. 'So, just supposing we're wrong and the Replicators came and infiltrated the city. Could we overload a naquadah generator to disable them the way we did with the Ancient nanovirus?'

Rodney winced, no doubt recalling the several hours he'd spent thinking he was going to die, then shook his head. 'I know a pulse shut down Elizabeth's nanites after Niam infected her, but those nanites were isolated units, and hadn't replicated enough and formed strong enough bonds to take complete control. The sheer numbers involved in human form replicators means they have an immunity to the effect of an EM pulse. What we would need to do is create a new disruption frequency to break the bond between each individual nanite, and we'd need a way to ensure they were all caught in the disruption field at the same time so they couldn't adapt and resist it.'

'And you can do that, right?' Sheppard said hopefully.

Rodney zoned out for a few seconds, giving the matter some thought. 'Yes. If I could find the right frequency, then we could do something similar to what we did in the jumper on Asuras. I could program it into the ARG crystal, and then change it for the one that generates the city's shields. As long as we can extend the field to cover the entire city, I should be able to get it to sweep through as far out as the full extent of the shield.'

'Sounds good.'

'Well, it would be...if I had enough time to do it. I'm still working on reprogramming Elizabeth's nanites so they can be shut down and leave her alive. Are you changing my priorities again?'

Sheppard chewed pensively on his bottom lip. 'I may be, yeah.'

'Oh, well let me know when you decide,' McKay hissed.

'I'm changing them,' Sheppard announced. 'I want you to work on the disrupter andElizabeth's nanites.'

'Oh, okay. And when did we add another twelve hours to the day?' McKay spat, folding his arms over his chest and glaring at him.

Sheppard wasn't at all fazed by his tantrum. 'It's all about time management and delegation, Rodney. Oh, and just out of interest, if we couldn't get the disrupter up and running, and if people on Atlantis were to be infected by nanites the way Elizabeth was, we could shut them down with a naquadah blast, right?'

'Yes. As long as one of us could get to a jumper and get it up to the right height, and as long as we caught the spread early enough,' Rodney agreed, calming with the distraction of the question.

'Okay. Thanks, Rodney. If you could look into that disrupter problem, I'd be grateful.'

He began to walk away, but Rodney called after him. 'You don't think the Asurans are finished with us yet, do you?'

Sheppard turned to face him again, wondering how much to say. He wanted to tell his friend about the dreams he was experiencing that constantly pointed to the dangers of having Elizabeth on board Atlantis, but he seriously doubted Rodney would sympathise. He kept his answer simple.

'I don't know any more about the Asurans' plans for us than you do, Rodney. All I do know is I can't think of a single reason they would have let Elizabeth go so soon that doesn't lead me to the conclusion that this is some kind of ambush waiting to happen.'

'Well, I've been doing a lot of work on those nanites since you asked me to reprogram them, and there is absolutely no sign they are in any way different from when she went on the heist to Asuras.'

Sheppard couldn't help but smirk at the scientist's assuredness. 'But you didn't have full control of them then, McKay. If I recall, you couldn't activate the 'kill' switch when we needed you to and you had no idea why,' he pointed out.

Faced with that evidence, Rodney had to concede. 'No...no...that's true. But they certainly aren't communicating on any subspace frequencies, so they're not giving our position away.'

'Maybe they don't need to,' Sheppard muttered, pondering just how much damage the nanites in Elizabeth alone could do if they began to spread.

'The nanites are showing no signs of acting under their own intelligence, Sheppard. You're worrying about nothing,' McKay tried to assure him. 'I wrote their code myself. They are no threat to us as they stand.'

Sheppard forced himself not to roll his eyes at the sound of Rodney's arrogant assertions. Much as he knew Rodney was right that the nanites were safe as long as they kept doing just what they were doing now, he also knew his subconscious was telling him there was a risk here, a danger that he shouldn't ignore. Still, until he saw signs of a real problem, there was no point in alarming Rodney with his fears, so he just nodded his agreement. 'I know, Rodney. Like you said, we just have to hope the other Replicators don't find us, and then we're home and dry.'

'Exactly,' Rodney said, giving him a lop-sided smile. 'I'll put some time into that disrupter, though –just in case.'

'That would be good, Rodney.'

'Er, are you going to get some breakfast now, 'cos if you are I can join you.'

Sheppard checked his watch, but decided 05:30 hours was just too early to start eating yet. 'No. I thought I would go check out things up at the control room, maybe run through any security issues with Major Lorne, then I'll get an update on Elizabeth's condition. Why don't I meet you there in an hour?'

'Okay. It's a date!' Rodney grinned, then cringed as Sheppard shot him a shrivelling look. 'Of course, by that I didn't mean a 'date' date...oh, you know what I meant!'

'See you later, Rodney,' Sheppard said, heading out the door before he laughed. Rodney really was bad at the whole friendly banter thing; even worse than he was, and he hadn't thought that was possible. That was probably why they gelled so well – two socially challenged individuals supporting each other through the minefield of friendship.

On his way to the control room, he stopped and stepped out onto one of Atlantis' many balconies to enjoy a few moments of the early morning air. The sky was blue, but broken up by cirrus clouds reflecting the warm tones of the sunrise. It was a beautiful view, but he couldn't fully enjoy it until he'd ascertained there was no Asuran ship lurking among the wisps of colour. His subconscious was warning him something was coming; his sixth sense for trouble had kept him safe so far in situations where others had perished, so he couldn't ignore it now. He just hoped Elizabeth wasn't central to whatever trouble was looming as his dreams were suggesting she was. She had to survive this.

After coming so close to losing her he realised how desolate Atlantis seemed without her there. The city was ailing, and it felt like fixing it depended on fixing her. Her dream had brought this place to life, and he hoped the nightmares he was now troubled by weren't a sign that it was all about to come to a terrible end. Whether the bond he and Elizabeth shared was more than friendship, he still wasn't sure, but he felt a strong connection to her, something he didn't want to lose again if it was in his power to stop it.

For now, he would have to take his mind off things by carrying out his duties, and later he would watch the feedback from the cameras in the isolation room again. Painful as it was to see her cooped up that way, it was more painful to speak with her face to face right now. Everything that had happened over the past week had unlocked feelings in him he hadn't realised he'd been suppressing, but now they had definitely surfaced, and were raw like an exposed wound. What was worse was the fact Elizabeth seemed to feel the same confusion, and now he was aware of that, distancing himself seemed all the harsher. But it had to be done. He was the current commander of Atlantis; he couldn't put himself in unnecessary risk or allow himself to become distracted by personal issues when so much was riding on him to get them all through this.

'Colonel Sheppard. Ms Shen of the IOA wishes to speak with you. I've been asked to patch it through to your office so she can talk to you in private,' a young female voice said through his earpiece. He recognised it as one of the women who worked in the control room, but whose name he'd neglected to learn. He made it a priority to do that today. He needed to be more personable with them all now he was in charge.

'Copy that. I'm on my way,' he replied, pushing back from the rail.

Taking a last, deep breath of the morning air, he ducked back inside to get the chat with the IOA out of the way. He'd been dreading this moment, and hoped they would allow him the extra time needed to find a solution to the nanite problem before insisting they be shut down. Now, it was time to find out just how accommodating they were willing to be

*****

When he got behind his desk and activate the channel to the SGC, he found Xiao Shen gazing back at him, looking as pristine and composed as she always did.

She gave him a tight smile, though her eyes remained cold. 'Good morning, Colonel Sheppard. I hope I didn't disturb you calling so early in the morning.'

'Not at all. I was already awake,' he assured her, giving her an equally unfriendly smile.

'I see. I suppose there is a lot to do there at the moment. How are the repairs coming along?'

'As quickly as can be expected,' he replied before deciding to cut to the chase. 'Have you reviewed the interview with Elizabeth?'

Shen straightened up in her seat, apparently surprised by his directness. 'We have,' she told him. 'In fact, we spent many hours discussing the matter. You do realise how serious a threat Dr Weir now poses to the security of Atlantis?'

Sheppard bit back the urge to ask her just how big an idiot she thought he was, and kept his response to a diplomatic, 'Yes, we all realise that. As you know, she's being kept in isolation, and anyone making physical contact with her is expected to follow full hazmat protocols. The nanites can't spread even if they wanted to, which, apparently, they don't.'

'So you feel the situation is contained for now?'

He ignored the unease that churned in his gut at the sound of that question. 'In my opinion, yes.'

'So as yet you see no reason to deactivate the nanites with immediate effect?' Shen asked, her eyes showing no sign of compassion as she said those words, as if she were talking about killing off a computer virus and not a human being.

John recognised the look as that of a person who could happily hide behind rules to commit the most heinous of acts if it were deemed necessary. Well, she might be prepared to let Elizabeth go, but he wasn't about to give up on her just yet. 'No. Both Drs McKay and Keller are monitoring the nanites on a regular basis, and there has been no change in their function. We will, of course, review the situation should that change. At the moment I have Dr McKay working on a way of healing Elizabeth using her own cells so we can shut the nanites down without killing her. I think she deserves that chance, don't you?'

Shen didn't answer that. 'And if deactivation of the nanites became the only viable option, would you be able to authorise that?'

Her eyes burned into him, and Sheppard realised what she was referring to. 'If the lives of the rest of the crew of Atlantis depended on it, I would have no hesitation,' he assured her.

'Are you certain of that, Colonel? It has come to our attention that your relationship with Dr Weir might be more...complicated than either of you has declared.'

Sheppard sucked in his cheeks and struggled to hold back the rant forming in his mind. The IOA had never been completely happy with the arrangement in Atlantis, and he certainly wasn't the first choice for military command. Now they probably thought they had a reason to finally remove Elizabeth from the picture, and perhaps him, too. Once again he kept his answer as civil as his growing anger would allow. 'I'm not sure what you're basing this assumption on, but I can assure you the relationship between myself and Dr Weir has never been anything but professional. If you're looking for a reason to remove me from my post, you're going to have to come up with something better than that.'

Clearly unimpressed with his tone, Shen brought their discussion to an abrupt halt. 'I believe I have said all that needs to be conveyed to you at this time, Colonel Sheppard. Continue the good work. Oh, and I would very much appreciate it if you could arrange for Dr McKay to brief us on his progress in the next scheduled update.'

Before he could respond the laptop screen went blank, leaving Sheppard with the almost irresistible urge to stamp it into oblivion. How dare that woman tarnish Elizabeth's character when she was already suffering so much? He didn't mind the bashing his own ego had taken because he was in a position to defend himself, but Elizabeth wasn't, and Shen didn't seem to care.

He sorely hoped McKay could pull off the miracle they needed and fix her, that way the IOA wouldn't get the opportunity to replace her after all. That would really give Ms Shen something to be so po-faced about.