Rodney had managed the grand total of three hours sleep before guilt drove him from his comfortable bed and back into the lab to begin working again. The new sample of nanites taken from Elizabeth only twenty minutes before his arrival in the infirmary that morning was doing nothing extraordinary; there seemed to be no hint of aggression in their behaviour, it just wasn't exactly what he'd programmed them to do.

Having watched them, poked them with various implements, simulated their current behaviour and run possible scenarios through the system, he still couldn't figure any reason for their change in behaviour.

He sat back from his workstation, rubbing his eyes to try and clear away the bleariness. He needed to get some proper sleep, but until this business with the nanites was unravelled to his satisfaction, he doubted he was going to get it.

04:33 am his laptop clock told him. Maybe he would just get his head down on the desk for a while; a power nap would soon have him firing on all cylinders again...

The smell of coffee permeated his nostrils as the scientist blinked himself back into consciousness. A mug stood steaming in front of him. Where did that come from? he wondered, lifting his head up from the counter so he could fully appreciate the aroma. Ahhhh, bliss!

'I thought I might find you here, so I brought you a coffee,' he heard his Czechoslovakian colleague call from somewhere behind him.

Rodney checked his watch. 05:37am. Had he really slept for an hour? His head throbbed, protesting that he was forcing it to work again so soon. It really didn't want to tell him whether his calculation of the passage of time was correct, or whether or not four hours sleep was feasibly enough to function on. It just kept trying to drag him back to the sleep he so badly needed.

In rebellion, Rodney snatched up the mug and took a swig of coffee. It was bitter tasting and strong, and burned his tongue as it hit it – just the way he liked it. 'Thanks for this, Radek,' he said, lifting his cup in salute.

'You're welcome. What're you working on?'

Rodney sighed, leaning back in his seat and raking his fingers back through his hair. When he'd come to Atlantis it had been much thicker than it was now, and he briefly wondered how much of its loss could be attributed to Mother Nature, and how much was purely down to stress. 'Elizabeth's nanites are functioning outside of their programming and I'm trying to figure out why.'

'What!' Radek was out of his seat and standing beside him before Rodney could even blink. 'Why didn't you wake me?'

'Because Sheppard told me to get some sleep, and I only started working on this a couple of hours ago myself. It seemed pointless to deprive you of sleep, too.'

Radek gave him a grim smile. 'For something this important I am willing to forego and hour or two,' he told McKay. 'I think you should bring me up to speed.'

'There's not that much to tell. They've replicated, but not in any quantities we need to worry about, and they've moved into Elizabeth's immune system. Keller thinks they might be trying to stop some kind of attempt by her body to reject the nanites, and she could be right...but she might not be. I just have the feeling this is the start of something bigger, and so does Sheppard.'

'Have you studied the coding to see if anything's been altered? Radek asked.

Rodney rolled his eyes in the Czech's direction. 'Yes...of course I have, Radek. I'm tired not retarded!'

Radek held up his hands in mock surrender. 'Sorry I asked.'

Sighing, Rodney ground out a reluctant apology. 'No, I'm sorry. You're right to go back to basics when you can't find the answer.'

'You want me to check the coding for you? A fresh pair of eyes might help and I figure I've had more sleep than you, so I can concentrate better than you can right now.'

'Oh, you're just loving this, aren't you?' Rodney grumbled, sipping at his drink. 'You've been desperately trying to prove you're better than me for the past three years and now here's your chance.'

'This isn't about anyone being 'better' at anything, Rodney. It's about saving Elizabeth. I'm just more rested than you are. No one can be expected to solve something as complicated as Replicator coding on the pathetic amount of sleep you've had in the past week. Admit it; you're worried about her.'

Although he didn't much care for Radek's use of the word pathetic, Rodney supposed it did suit the situation. 'Okay, fine, I'm worried. You start checking through it again, and I'll just sit here looking redundant, shall I?'

'Actually, I think I finalised the repairs to the control chair last night. You could look over those and make sure they encompass everything you need for that remote jumper before I implement them if you like.'

Rodney knew Radek was just trying to make him feel better, and somewhere deep down in his cynical heart he appreciated the gesture. Unfortunately, that sentiment wasn't what came out of his mouth.

'Yeah, sure,' he huffed, taking the data file Radek was holding out toward him. 'I'll just check the simple stuff, shall I? That way I can't do any more damage!'

Radek gave him a bemused smile and headed off to his own workstation to check the nanite coding while Rodney continued to grumble.

oooOOOooo

Sheppard walked the corridors of Atlantis, heading to the infirmary. He'd managed a few hours of sleep and now wanted an update from the infirmary staff. When he got there, Marie was on duty while Keller got some much needed down time.

'Morning. Any news on Elizabeth's condition?'

Marie shook her head. 'Nothing much. The new nanites are still attached to her immune system, while the old ones continue to keep the repairs in place. We've been watching her all night. She's been a little restless, but otherwise there's nothing to report.'

'Is she awake?'

'I'm not sure. But we can go and check.'

She guided him through to the side lab where the screen had been set up for playback of the footage in her room. Elizabeth was just yawning and stretching her arms, clearly in the early stages of waking.

'I should go see her – find out how she's doing this morning.'

Marie nodded and gave him a sympathetic smile as if she knew how difficult it all was for him. 'You know where the hazmat suits are.'

After kitting himself up, Sheppard trudged his way to the isolation room with heavy limbs and an even heavier heart. He didn't have the first idea what to say this morning. Last night had required him to be clear and efficient in his explanations, but now, this was time for him to be a friend, and lately that wasn't as easy as it used to be. He wished he could forget what she'd said in the interview, forget the questions it had forced him to ask himself about how he felt for her. When he'd first met her she'd been off limits. Then, they'd taken up dual leadership roles, and anything more than camaraderie was out of the question. But circumstances had changed; and he was afraid of the emotions now awakening in him for someone he felt was slipping out of his reach. He forced himself not to analyse what he was feeling; he couldn't afford to falter now.

When the guards let him in she was already sitting up. She smiled as he approached, causing him as much pain as if she'd landed a sucker punch. 'Morning, John. I might have known you'd be the first person to appear this morning. I see you opted for orange even though it isn't your colour.'

He fought to smile in return. 'How'd you sleep?'

'Well, I did have one or two things on my mind –'

'I can imagine!'

'— but I did okay, I guess. I imagine I got more sleep than you did judging by those dark circles under your eyes.'

'Well, you sure know how to make a guy feel good about himself,' he quipped, already beginning to tire of the suit. It felt heavy and cumbersome and he wondered how long would be considered a polite length of time to stay there with her since he couldn't wait to get the damned thing off again.

'Have there been any further developments in my condition?' she asked.

He shook his head, grateful that she seemed only too happy to deal in facts rather than wallowing in self-pity. 'Nothing as yet. They're still invading your immune system, but the numbers haven't increased to a point where we need to worry, and they seem to be holding steady. I imagine Rodney is already at his desk working on a solution, so, who knows, later today this may have all blown over.'

'I think that's being a little optimistic, even for you.'

He shrugged. 'Rodney has a knack for pulling miracles out of his a – hat, so don't give up on him just yet.'

He could see her struggling with the urge to laugh. Obviously he hadn't covered his gaff quite as well as he'd hoped. But, when she did speak, her response wasn't as positive as he'd hoped for. 'You know this is all going wrong, don't you?' she said sadly, her huge eyes meeting his and filled with so much pain he felt his heart would break for her. 'Eventually, one way or another, I will cease to be.'

He shook his head, unwilling to accept what he knew was most likely inevitable. 'He'll figure something out.' He approached her, standing before her and resting his hands either side of her legs on the bed. 'You just keep fighting to remember who you are, and let us worry about the rest.'

As he looking into her eyes a strange glaze passed over them, and then was gone again just as quickly. He pulled back, hoping it was a trick of the light or a figment of his overtired brain, but something had changed. She was smiling now, but not the sad smile she'd forced on for the past few days; this was a malevolent sneer, much like the one Teyla had worn when taken over by the Wraith.

'You can continue to hope, but whatever you try will be in vain,' Oberoth's voice said from Elizabeth's lips. 'You cannot hope to stop us. Your intellect is ludicrously small in comparison to ours. We will be victorious.'

Though shocked, Sheppard reacted strongly, the sudden emergence of the Asuran leader's voice not coming as a complete surprise to him. This was only confirmation of what he had suspected all along. The Asurans had altered her and taken control. 'Let her go, you bastard!' he growled. 'Let her go, and I promise I won't hunt you down and destroy you.'

'You are mistaken, Colonel Sheppard,' the voice said confidently. 'You cannot come after us. Already, nanites are spreading throughout your city, taking over everyone and everything in Atlantis.'

Anger spurring him into an irrational reaction, Sheppard launched for her, grabbing her throat and squeezing. All he could think of was freeing her from Oberoth's grasp, even if that meant killing her. Unfortunately, he hadn't factored in the newfound strength the nanites afforded to her. She jammed her hands into his chest, knocking him backwards and sending him sliding across the floor until he collided with the door.

He expected it to open, and to feel the strong hands of two marines pull him to safety, but it didn't happen. Elizabeth jumped off the bed, padding barefoot across the cold floor toward him. 'Everything and everyone in Atlantis will fall,' she said in her own voice now, her fierce gaze burning into him. 'And you, Lantean, will be spared until you have witnessed it all.'

'I...I'm not a Lantean,' he stammered, his brain still spinning from the impact. 'You know that.'

She bent down to him, grabbing handfuls of his protective suit to pull him closer to her. Her eyes glared at him just as Oberoth's had when they'd made their escape from Asuras, leaving Elizabeth behind. 'You are a direct descendant of the Lanteans. Only someone bred from pure Lantean lineage could have such a strong genetic link to them. In the absence of your predecessors, you will bear witness to the final destruction of the cornerstone of their empire.'

That said, she pushed him away, thudding his head against the door again and sending him tumbling into unconsciousness...

Sheppard woke to the sensation of sweat-dampened sheets and clothes, but recovered more quickly than he had on previous days. The nightmares were becoming so much a part of his nighttime routine he would have felt deprived without them. He climbed out from beneath his sheets, stripped both himself and his bed down, and headed into the bathroom to get cleaned up and start his day.

After popping into the infirmary to check on Elizabeth's status, he headed to his office and read a couple of those pending reports. He felt guilty for not going to see Elizabeth in person, but the dream was still fresh in his mind, and needed to change the pattern of events out of some weird and newly discovered superstitious facet of his personality. Though vowing to see her later eased his conscience a little, he couldn't fully override the feeling he was letting her down. But what could he say? Nothing that the medical team couldn't tell her anyway.

He took breakfast alone – deliberately so. He waited until the time his teammates usually ate had passed and then added an hour, just to be absolutely sure they were gone. No one came to look for him, which he took as a sign that they recognised his desire to be left alone. His feelings about Elizabeth and the nanites were dragging him down. He wouldn't be good company, and the last thing he wanted was to try to be upbeat for everyone else when he felt so low. Added to that, he still wasn't sure how to deal with Teyla yet...

He found a table in a quiet corner and drank some orange juice while he waited for his infamous appetite to kick in. Today, he didn't feel hungry at all, but knowing he would need the calories to keep him going for the next fourteen hours at least, he forced down some toast while trying to ignore the mild nausea the intermingling aromas of eggs, waffles, pancakes, bacon, and various other breakfast foods evoked in him. Once he'd picked at half of his meal, he surrendered and made his way up to the control room for an update.

Chuck talked him through all the latest long-range scans they'd run, none of them showing anything untoward. Sheppard nodded as he listened, knowing from the tone of voice the technician used that the information he was giving him was nothing to be alarmed about. Though he tried to concentrate, his mind constantly drifted to the memory of seeing a city ship approaching Atlantis in one of his earlier dreams. He had to fight the urge to rush out onto the balcony and check the skies again.

Duties successfully performed there, he headed on to the labs to catch up with Rodney. He found both him and Radek scouring the nanite coding. They were bickering as they always did, but it was mostly good-natured and not particularly hurtful, so, figuring it was best to leave them to their work, he warned them to play nice and went on hi

Today he was restless. Nothing in Atlantis felt right. For some reason, even the background hum that always accompanied him sounded discordant, as if the city was trying to tell him something was wrong. The alarms might not be sounding, but he instinctively knew it was true.

Plucking up courage, he decided now was as good a time as any to visit Elizabeth, and so headed for the nearest transporter to take him to that level. As he tried to think of what he wanted to say to her, he heard footsteps hurrying to catch up to him.

'Colonel. We missed you at breakfast this morning.'

Teyla.

He turned to face her, wondering what kind of a reception he would receive. To his relief, she gave him a bright smile as she jogged to a halt in front of him. From her attire and the equipment she carried he could see she'd been training. 'You and Ronon been fighting already this morning?' he asked.

'Yes. We sparred before breakfast. I have been training with a number of the marines for the past couple of hours. What have you been doing?'

'I thought I should make a dent in the pile of work on my desk I've been putting off for the past several days,' he answered, and it was almost the truth.

'I see. And have you seen Elizabeth this morning?'

'Not yet, I was just on my way. I take it Rodney's updated you on the developments.'

She nodded. 'He has. If you do not mind, I would like to accompany you and visit with Elizabeth also.'

He shrugged casually, 'Sure,' but he was greatly relieved to know she would be there with him. Teyla could always sooth any situation with her calming presence. He felt sure Elizabeth would benefit from having her there while dealing with the issues her changing situation brought.

They reached the transporter and he activated the doors so they could step inside. 'You know about the need for hazmat suits now, right?' he asked, turning to face her just as she swung her Bantos rod at the side of his head and, after a blinding flash of light and pain, everything went black...