Sheppard's yelling hit Rodney's eardrums and set them ringing as soon as he got out of the transporter. He'd been on his way to the infirmary for something to perk him up when his friend's screams caught his attention. He immediately broke into an uncharacteristic run, arriving at the infirmary sweaty and short of breath. There, he found Ronon and a couple of the medical team pinning Sheppard to a bed while Keller secured him with wrist and ankle restraints, plus a strap across his torso that pinned his arms to his sides.

All the time Sheppard bucked and kicked and cursed at them, demanding to be released. It was a bizarre scene, one Rodney would never have expected to find, not even in his worst imaginings.

'What are you doing to him?' he hissed, motioning with his head for Keller to step aside with him. 'Is all this really necessary?'

Hearing his voice, Sheppard's wild eyes fixed on him out of everyone there. 'Rodney, you gotta get me outta here! They're trying to say I'm crazy. Don't listen to them; they're lying – they're lying!'

McKay backed up a couple of steps, driven back by the force of his words. 'Er...okaaayy!'

'We're not saying he's crazy,' Keller stated clearly, rushing back to the bed and struggling to tighten the final strap. 'He's suffering from a severe concussion that has left him delusional. We need to confine him to an infirmary bed until we're sure he isn't a threat to himself or anyone else.'

'A threat? This is Sheppard!' Rodney gasped. Sheppard was Atlantis' sentinel. He couldn't even consider the thought he might do someone any harm.

'He attacked me when I was heading for the mess hall,' he heard Ronon grumbled. 'It's not safe to let him out of here.'

'So post a couple of guards next to his bed until he's himself again!'

'I didn't do it, McKay,' Sheppard screamed, thrashing against his bonds. 'He shot me in the corridor on my way to see Teyla and dragged me here. You have to believe me! There's something wrong with them!'

'This is Sheppard we're talking about. You think two guards would stop him?' Ronon smirked to Rodney, ignoring the colonel's outburst.

Rodney supposed the big man had a point. This was the second time in just an hour he'd heard Sheppard accuse one of his friends of aggressive behaviour. And he had been rambling in the lab a short while ago, making very little sense. Perhaps this was the best thing for him. 'We can let him go once he's better though, right?' he asked.

'Once we've established he understands what's going on around him and accepts the truth, we'll take off the restraints,' Dr Keller assured him.

Rodney watched him struggling and cursing, flinching away again as the bed shook with the force of his thrashing. 'So, what's happened to him? Is it serious?'

'My guess would be some kind of breakdown, but we'll have to wait until Dr Heightmeyer's had time to assess him before we'll know for sure.'

McKay realised his heart was thundering against his ribs as he watched his friend straining at his bonds. Sheppard had always been a voice of reason and someone he leaned on for strength in times of trouble. Without him there to support him, Rodney felt...exposed.

'Could it be something else? A virus or something like that? I know how screwy I get when I pick up the slightest little bug – '

Keller shook her head, smiling grimly. 'I don't think so. He's displaying many of the classic symptoms of a break down; disturbed sleep, anxiety, changes in appetite, paranoia, seeing things that aren't there, violent behaviour...'

'Sounds like me on a good day,' he mumbled, wincing as Sheppard let out another torrent of abuse at those trying to calm him.

'I could admit you, too, if you're worried,' Keller suggested.

Rodney frowned at her. 'That was a joke,' he sighed, wondering how she could have missed that.

'Oh, right. Of course. Very funny,' she said, tossing him the briefest flicker of a smile. 'Now, if you don't mind – we're pretty busy here. Can someone get me a dose of Benzodiazepine to knock this man out! '

She made as if to steer Rodney toward the door, but he side-stepped her touch and headed towards Sheppard.

'Sheppard...Sheppard, it's me...McKay.'

Sheppard's head snapped up from the bed. 'McKay. Don't believe them. I'm not sick. They're Replicators...maybe all of 'em! Don't let 'em sedate me!'

Okay, maybe Keller has a point! McKay pondered,knowing there had been no sign of an Asuran vessel approaching the city at any time.'I think you need to get some rest, Sheppard. All this has been a bit too much for you. You should let the doctors help you,' he said, speaking slowly and clearly to be sure his friend would understand.

Sheppard's green eyes flashed with annoyance. 'Don't patronise me, you arrogant little –'

'You need to go, Rodney,' Keller advised him, raising her voice over the colonel's insults. 'I think he's finding your presence here...disturbing.'

'I'd say he's finding just about everything disturbing,' Rodney replied, his eyes bulging at the sight of Sheppard straining against his cuffs. It was a good thing they were thickly padded because he suspected the colonel wouldn't have stopped even if they were slicing his skin to ribbons. As it was, they were rubbing his wrists raw already.

'All right. Would you tell him I'll be back to see him later...once he's a bit more rational.'

'Of course,' she nodded, turning away to attend the beleaguered military man.

As he shuffled his way out of the infirmary, Rodney felt eyes burning into him all the way to the door. He glanced back over his shoulder to find Ronon glaring after him. Very slowly, a smirk curled the Satedan's lips, then he looked away, returning his attention to battling the colonel.

Rodney felt a shudder run the full length of his spine. Something about that smile was incredibly unnerving. The Satedan did have a somewhat cruel sense of humour, but even he didn't normally find Sheppard's suffering amusing. They were almost like brothers, unerringly protective of one another. Why would Ronon behave this way now?

Unwilling to challenge him on his odd behaviour due to his innate fear of pain, Rodney continued on to his lab. He didn't need a pick-me-up now; seeing Sheppard in that state had definitely been the wake-up call he needed. But he didn't have time to worry about everyone else. There was still a lot of work to do on Elizabeth's nanites if he hoped to get them in line and stop them adapting any further.

*****

Three hours and six cups of coffee later, Rodney continued to work with trembling hands, now completely wired on caffeine and power bars. His brain was tired but functioning well, at least as far as he could tell, yet the solution to the nanite problem still eluded him. Even Zelenka had given up on the challenge, telling him he had other things to check. It should have been complex but doable, but the more Rodney tried, the more the damned things seemed to lock him out. They appeared to be permanently stuck in the programming he'd provided to save her life after the accident, and now wouldn't allow him to alter them. The only changes possible were those they made themselves to protect her well-being.

There had to be something wrong in the way he'd written the program. He couldn't change them, yet they were adapting on their own. That was way beyond what he wanted them to do, and pretty scary considering what the Replicators were capable of.

Rubbing his tired eyes, he sat back and stretched, then scratched his ribs and straightened out his aching knees. All this sitting around staring at computer screens was crippling him. What he wouldn't give to be forced to have a stay in the infirmary...no, he reconsidered, remembering the treatment Sheppard had been undergoing when he'd last seen him, maybe not. A few hours in his own bed were definitely preferable to that.

Giving himself a second or two longer to rest his eyes, he got back to the nanite code, this time noticing something he hadn't seen before. It seemed obvious now when he looked at the screen, but one of the decimal points was a fraction larger than the others. Since it was the only anomaly he'd found, he figured he'd better correct it...though he couldn't imagine how the computer had changed the size of the text for one character. It was probably something Zelenka had interfered with earlier and nothing to do with the problem he was trying to solve.

Highlighting the error, he tried to delete and replace it, but found it wouldn't go. He tried again, three times, but the persistent dot would not budge. 'This is nuts,' he muttered to himself, deciding to stop wasting his time on the shortcut, and write in the instruction in a way the damned thing couldn't ignore. This time it didn't ignore it, but the instruction didn't do quite what he planned. Instead of disappearing, the decimal point expanded out into reams of data, spooling down his screen so rapidly he had no hope of keeping up with it.

'What the...' he breathed, as his eyes tried to lock onto anything whizzing past on the screen. He couldn't define anything specific in the way of instructions, but he could see it was Asuran, not the re-written coding he had created. 'Oh, this is bad...this is very bad.'

'What is bad, Rodney?' Teyla asked, taking him by surprise since he hadn't heard her enter the lab.

Surreptitiously angling the screen away from her, he covered the problem as best he could. 'Oh, I'm still getting nowhere with the nanites, that's all,' he lied, wondering why he felt compelled to be dishonest with her. Was he really going to let Sheppard's inane ramblings in the infirmary colour the way he treated his other friends?

'I do not think it is necessary for you to keep working on that problem when your skills could be put to good use elsewhere,' Teyla suggested, a hardness to the way she looked at him he'd never noticed before. A shudder ran up his spine again. Why would Teyla think leaving the nanites active inside Elizabeth was a good thing? She'd wanted them out of her as much as he had not a day ago.

'Er...yeah...you're probably right,' he agreed, closing the lid of his laptop. 'There are plenty of other systems that could use my magic touch.' He wiggled his fingers as he said that, but Teyla only arched her eyebrow as if she had no idea why he would do such a thing.

'That was me doing magic...you know...like a magician...I've told you about magicians before, right?' he said with a pained grin.

Teyla ignored the question. 'Sheppard has been setting your priorities for the past few days. Considering what has now happened, I think it would be wise to review operations and re-evaluate what is most needed.' Her eyes drifted around the room, finally stopping when they fell on the ARG resting on a workbench nearby.

'Well...I know Sheppard has gone bye-byes for the time being, but most of what he asked me to do actually made sense,' Rodney told her, feeling the need to defend the absent colonel.

'We will decide that now.'

He gaped back at her, troubled by her firmness. 'Who exactly is this 'we'?' he asked.

'Major Lorne and myself. We feel that if the responsibilities are shared between two of us, in the way that Dr Weir and Colonel Sheppard shared them, the pressure will be more bearable.'

'Okay, I can see the sense in having a dual leadership again, and Lorne is the obvious choice for military commander, but who decided you should join him?'

'You can think of someone more suitable?' she asked, narrowing her eyes in a way he could only interpret as menacing.

'No...I just thought the IOA might want a say in all this.'

'I am more than qualified to lead people than most in this city. Would you rather do it yourself?'

He shook his head. 'I...I didn't say that...'

'I'm sure you realise your skills lie elsewhere, Rodney. Much as I am certain you would make a good leader, you are a far better scientist than I could ever be.'

'Well, yes...how's Sheppard doing?' he asked, changing the subject.

'He is...as well as can be expected. Dr Keller is keeping him sedated for the time being until his mind is more settled. I fear it will take some time for him to recover his senses fully.'

'You really think he's that bad?'

'Dr Keller believes he is quite insane, and if I am honest, I would say I have seen this coming for some time. Sheppard carries so much guilt within him...a man can only bear so much.'

That didn't sound like the Teyla he knew. First, she'd told him to stop working on the nanite problem, now she seemed determined to undermine Sheppard's authority. Those were two things he would never have expected to hear from her.

'Well...I've got a thousand other things I need to be doing,' he said, hoping she would take the hint.

'That is all right, Rodney,' she said, resting her hand on his. 'Major Lorne and myself need to contact the IOA and give them an update on the change in circumstances following Colonel Sheppard's...indisposition.'

'Good, good...you run along and do that then!' he said, snatching his hand back and grinning almost maniacally. She eyed him oddly, glancing momentarily at the ARG once more before making her way out of the lab.

McKay let out the breath he'd been holding for the last few seconds in one huge sigh. Sheppard had been right; there really was something weird going on with Teyla. He'd never seen her behave that way before, and he'd never once known her to have a bad word to say against Sheppard. But the colonel had said they were Asurans, surely that couldn't be right?

Checking no one else was nearby, he began to reprogram the sensors to pick up the energy signature of Elizabeth's nanites. It took a few minutes to do it, then he sat back and watched his screen, waiting for the results.

The scan picked up Elizabeth first, as she was the strongest source of the units, then he knew the samples in the lab and the infirmary would show up, too. What he didn't expect were the dozens of other dots suddenly popping up all over the city, some of them quite faint as if only a few nanites were present, others much more substantial. But the really scary thing was that new dots kept appearing every few seconds. The infection was spreading through the crew as he watched in open-mouthed horror.

'Oh crap!' he gasped. 'He was right...well, kind of. How the hell did this happen?'

An alarm sounded on the laptop beside him. At first he ignored the persistent and somewhat shrill beeping because he was so enthralled by the saga unfolding on the screen. Then, the noise wheedled its way into his screaming brain, forcing him to acknowledge it. It was the disruptor frequency program; it had found something.

McKay spun the laptop round to face him, frantically studying its findings. He ran the frequency through the numerous simulations he'd set up, including one with the most up to date information gathered from Elizabeth after the nanites began to act on their own initiative, and each time it was successful.

'Ha!' he barked, his face erupting into a victorious smile. 'I did it. I actually did it.'

But there was still a problem. If Teyla and Lorne, and, come to think of it, everyone else likely to be manning the control room were already infected, it was highly unlikely they would let him in there to replace the city's shield crystal with the re-programmed ARG control crystal and do the work he needed to carry out to make the disruptor work. So what now?

His eyes darted about the lab as he tried to think of some way of getting to the shields. He supposed he might be able to carry out the reprogramming necessary to accommodate the crystal and it's function from another terminal in the city, but it might be detected, and he still needed to swap over the crystals.

As he tried to think of some distraction that might divert attention from the shield systems, his eyes finally came to rest on the tablet with the jumper diagnostics he'd been running since accessing the remote systems. A jumper! He could do the same thing he'd done on Asuras, except that had been a relatively small field, and that was all the power source on the jumper had been able to manage. Of course...there were ways of augmenting power systems, and it wouldn't take that long...not for a genius like him. All he needed was a quick burst of power that would last long enough to sweep the entire city in one go. So, he had to get the reprogrammed ARG crystal and a naquadah generator into a jumper so he could set the field off throughout the city.

Wracking his brain for where he could find a naquadah generator no one would miss, he remembered a project one of his team had been working on prior to all the problems of the past several days. He was pretty sure no one would check it for the next few days because everyone was busy repairing the city, so he could grab that one with little difficulty...theoretically.

Half an hour later, Rodney was sitting in the pilot seat of Jumper One. He'd attached the naquadah generator to the power relays, taken readings to ensure it was generating enough energy to help the shield spread, and was now finalising the instructions of what the ship's shield should do once activated. Unlike on Asuras, where he'd needed the shield to simply extend downwards, here he needed it to extend in all directions, encompassing the whole city and everyone in it in a matter of seconds before the Replicator nanites could adapt. He'd just keyed in the final codes when he heard a voice in his earpiece.

'What are you doing, Rodney?'

It was Zelenka.

'Er...nothing much...why?'

'I thought you had already accessed the remote commands for this vessel?' Radek asked, now walking up the rear ramp and planting his hands on his hips as he waited for an explanation.

'Well, I was just checking them out again before doing a test run...what do you want, Radek?'

'I'm having difficulties with the city's shield. As you know, it was up and running and fully extended, but the whole thing now appears to be collapsing.'

'What...collapsing! How is that possible?'

'I don't know, Rodney. That's why we need you to look at it.'

'So you have absolutely no idea what's gone wrong...I thought you were supposed to be smart!'

'Well, yes...but not as smart as you.'

It suddenly occurred to Rodney that Radek should have had some idea what was happening with the shields, and would never have dared to come before him claiming to be so clueless. And he also realised the Czech was standing on board the jumper, and as such would not be caught by the expanding disrupter field. He had to get Radek off the jumper, run some simulations, and then set the damn thing off. He couldn't afford to be found out, and he couldn't afford anything to go wrong.

'Okay...you go on ahead and I'll catch up with you,' he said, hoping to rid himself of the diminutive scientist long enough to make sure everything was as it should be to set off the disrupter.

'Teyla asked that you come now...I really think you should, Rodney. We can't afford to be without the shield for long.'

Dammit! Apparently, Zelenka was determined not to leave him working on this project. Did the nanites inside him somehow sense when something was a threat. Glad the Czech hadn't seen him inserting the ARG crystal into the jumper's systems, Rodney figured he was going to have to humour the man and sneak back later.

'All right, fine. I'll come. But I swear if it's something obvious I'm going to demote you.'

'Whatever you think, Rodney. But you must come right away.'

McKay shutdown his laptop, but left it on the pilot seat, keen that everything should be there for him to run a simulation the moment he could break away from the shield repairs.

'You know, you probably shouldn't bother with the jumper amendments considering Colonel Sheppard has been declared unfit for duty,' Zelenka said as they walked.

'Oh, this from the man who was willing to believe anything he said yesterday,' Rodney blustered back, keeping up the facade of their normal bickering.

'Well...obviously I was wrong about that. He clearly poses a danger to everyone in this city. It's essential he's kept out of the way while we work.'

'Yes...yes,' McKay nodded, seeing through their transparent ploy so easily now he wondered how he could ever have fallen for it. 'He's completely lost the plot, poor guy. Good thing Lorne and Teyla are in charge now. Things should start improving around here soon.' He could feel little rivulets of sweat breaking out on his forehead as he strained to maintain both the ruse and his nerve. He was a terrible liar, always had been; he wondered how long he could keep it up.

As they were passing the labs it suddenly occurred to him that he appeared to be the lone free-thinking person still able to move about the city. That meant if he went to the control room he would be surrounded by infected people with little chance of getting away from them to carry out his plan. And suddenly, the thought he was the only one making that stand was terrifying for him. He was a scientist, and fighting still wasn't something he felt comfortable with on a physical or ethical level. Sure, he could push it down when necessary, but the fear always surfaced, no matter how hard he tried to keep it down. Sheppard, Teyla and Ronon were naturals, able to mentally detach themselves from the deeds they had to do to ensure their success. But the obstacles he might come up against were all people he knew, at least by sight even if he couldn't remember their names. He wasn't sure he could do what it might take to get back to the jumper bay if any of them stood in his way.

But there was someone who could.

Making a big show of rubbing his forehead, he stopped walking. 'You know, Radek. I have a terrible headache. I think I might head over to the infirmary and get something for it. Why don't I meet you at the control room when I'm done?'

Radek raised his eyebrows, but didn't question him. Perhaps headaches were a good sign as far as the infected personnel were concerned. 'Okay, Rodney. But no sneaking off to finish working on that jumper. We need you fixing the shields.'

'I'll be right along,' Rodney promised, grinning inanely as he watched Radek shuffle away.

Once he was around the corner, Rodney bolted back toward the lab. He needed Sheppard, but to reach him, he had to use one of the colonel's own ideas. If only he'd been as willing to listen when the colonel had first asked him to do it those several long days ago.