This is the tag fic for The Real World. There was no real way to get physical whump into this episode so I've gone with good old-fashioned emotional angst instead! Hope you enjoy...

He wasn't there when she woke up.

Carson's staff, their faces stern behind the hazmat masks, had pulled him bodily from Elizabeth's isolation tent and marched him straight into an isolation area of his very own. This one had walls instead of plastic sheets, a solid door instead of a simple zipper and clear windows to allow observation. The first thing his escorts did was take away his gun and as he saw the fear and distrust in his eyes it hit him hard, like a punch to the gut; the risk he had taken. It was worth it though, he told himself as they left the room, the door sliding shut behind them with the distinctive sound of the lock engaging. It had to be. She would make it. She would. The alternative was… No, he couldn't… he wouldn't think about that. They'd lost enough… he'd lost enough and every death was a burden, a weight on his soul.

He'd lost men under his command, civilians he was supposed to protect, even his own CO, but if he lost Elizabeth… if he lost any of them, of his family… The fact that he felt even the slightest bit thankful that the people they had lost, the people he had failed to protect, had not been those he had cared most about, was yet another burden for him to carry, another millstone of self-recrimination. His team… Elizabeth, Carson… they were all he had.

He'd opened his soul, as best as he was able, to Teyla on the Daedalus, sharing with her the bare, painful truth, and it had been no maudlin dramatics, no heroic gesture, when he'd said he would die for any of them. He would. And even that was a reason for guilt; an ugly little voice telling him that that was the coward's way out, that he was simply running from his responsibilities… that dying was easy, easier than living with the pain of loss.

He paced the small room restlessly, his body stiff with tension, his mind racing, wondering what was happening just down the hall… he spun on his heel as the door hummed open to admit more hazmat-suited medics, rolling an ancient scanner into the room with them.

"How is she?" he demanded. "Has there been any change?"

Their expressions were guarded, non-committal, their voices muffled by the suits as they side-stepped his questions with vague platitudes and reassurance.

"You'll need to lie down, sir."

John felt frustration pulling his shoulder muscles into knots. He knew this was necessary. He'd put himself in this situation, done it willingly in the faint hope of getting through to Elizabeth, giving her that small connection that could help her to hold on, to fight. But that knowledge didn't make this any easier, didn't quell the nerves in his stomach, the tiny, spiteful thread of fear that lurked at the back of his mind, telling him that it was too late, that they were going to lose her and there was nothing he could do about it. Being cut off like this, not knowing what was happening, was torture and his movements were jerky with impatience as he reluctantly hoisted himself onto the exam bed and laid back stiffly.

As tense as he was, the combination of bulky-suited medics bustling around the bed, their faces all but obscured in their protective hoods, and the heavy arm of the scanner looming over him as it was swung into place over the bed felt threateningly claustrophobic and it was all he could do to hold himself still and not jump from the bed and make a run for it. He fisted his hands into the starched white sheets beneath him and gritted his teeth as the scanner powered up with a low hum and began its steady hover up the length of his body.

As he lay there, biting down on the fear and worry, watching the sleek white surface of the scanner slowly block out his view of the ceiling above, he couldn't help but think back to the last time he had lain fully-clothed on a medical bed, the gentle hum of the scanner vibrating overhead. He'd kept his eyes closed that time, focusing his attention inwards, hyper aware of his body and the way it was starting to feel… different. He frowned. Much as Elizabeth had doubted his assertation at the time, he had been able to feel something happening to him, feel the virus slowly changing him. He wondered if it had been the same for Elizabeth, if she had been able to feel – was still able to feel – what the nanites were doing to her. And what if the nanites were now in him, too? Would he feel it? Would he…?

He closed his eyes and forced himself to try and relax, pushing out a long, slow breath and focusing his attention inwards. He concentrated, feeling the rise and fall of his chest with each breath in and out, the weight of his limbs pressing into the mattress of the bed as he tried to relax his muscles. He felt tense, his body thrumming with nervous energy… but otherwise normal. There was no sense of wrongness, no indefinable awareness of gradual physiological changes that would eventually wreak havoc on his body, his mind… He opened his eyes abruptly, a sigh of frustration escaping him. If the nanites were inside him now, then he had no awareness of it.

Maybe Elizabeth hadn't either… she'd seemed perfectly fine. Hours had passed since Niam's attack and she'd shown no symptoms, no hint of suspicion that anything was wrong… right up until she'd simply collapsed in the control room, a dead weight in his arms as he radioed frantically for help. He couldn't help but dwell on that terrible moment, on the terrifying suddenness of her collapse, the feel of her body utterly limp in his grip. For a moment he hadn't even been sure that she'd been breathing and cold fear had gripped his heart. He'd laid her gently on the ground, instinctively applying the field triage training that had been drilled into him as he checked her airways, breathing and pulse. He'd been operating on autopilot, his subconscious mind pushing him into action even as his higher brain function struggled with shock and fear.

He'd had the luxury of indulging that shock for about ten minutes… the amount of time it had taken for Carson to get to the control room, load Elizabeth onto a gurney, get her back to the infirmary and run his first scan. From that moment on, the city had been on high alert and John was officially in command of the Atlantis Expedition. The appearance of the nanites on that first scan had thrown the infirmary into chaos, off-duty medical staff who they could be reasonably certain had been nowhere near Elizabeth being called in to gear up in hazmat suits while Carson himself had rapidly enacted isolation protocols and herded everyone who'd been near Elizabeth, including John, into a secure section of the infirmary.

They'd scanned everyone, starting with Carson who hurried off immediately to suit up and return to his patient. The scans had been clear, even John's who'd held her in his arms, who'd touched the bare skin of her arms, her neck, her face as he'd laid her on the floor of the control room and checked to be sure she was still alive. He didn't know why the nanites hadn't spread then and he didn't know whether they had spread this time. Could he have dodged the bullet twice? Or was what had happened to Elizabeth happening to him now? Were the tiny, aggressive robots multiplying and proliferating in his body, waiting until they were large enough in number to attack his brain, to drop him where he stood and leave him helpless as they slowly took over his body?

The scanner ground to a halt with a decisive clunk and he sat up abruptly, turning his attention to the hazmat suit holding the datapad.

"Well? What's the verdict?" His voice came out rough, tinged with impatience.

The medic – the bluish lights lining the faceplate tended to wash out and distort color but he caught a glimpse of what looked like a stray curl of red hair and realised belatedly that it was Dr Nielsen under the helmet – looked up from the scan results and gave a cautious nod. "It looks clear, Colonel," she told him.

The surge of relief he felt was immediately drowned out by the need to get out of here, to get back in there and find out what was happening. Surely they'd have told him if something had… if…? He made to slide from the bed and found a thick-gloved hand on his shoulder, stopping the movement.

"I'm sorry, Colonel Sheppard. You can't leave yet."

He stared up at the burly medic – Steiger, wasn't that his name? – and felt frustration simmering towards anger. "Why not?" he ground out. "The scan is clear…"

"We don't know how long it may take for an infection to show up on the scans," Neilsen interrupted and he heard genuine regret in her muffled voice. "There was no sign of any nanites when we scanned Dr Weir's neck following the replicator's initial attack on her," she explained. "It could take hours for a small number of nanites to reproduce enough to become visible to the scanner."

"Hours?" John's stomach lurched.

Steiger's hand was still firm on his shoulder. "Sorry, sir," he rumbled. "You're to remain in isolation. Dr Beckett's orders."

He felt his shoulders sag with defeat, the stress and tension of the past few hours suddenly catching up to him and draining the strength from his body. The momentary reprieve had been just that; momentary, fleeting. He could still be infected. He was still a security risk. And he was still locked up, cut off from his team, from Elizabeth who at this very minute could be… He pushed that thought away wearily. Whatever was happening just down the hall, there was nothing more he could do to help. He didn't protest when Neilsen mentioned blood tests, obediently rolling up his sleeve for the needle. He sat on the exam bed, his thoughts distant, only vaguely aware of the continued bustle of the hazmat-suited medics.

He was brought out of his brooding by a sudden banging sound; a fist on glass. He looked up, surprised to see a broadly grinning McKay pounding on the observation window. McKay's voice was muffled by the thick glass but nonetheless John's heart skipped a beat as he read the words on Rodney's lips.

"She woke up!"

McKay's smile was glorious, heartfelt, and he felt an answering grin stretch his face as a little bit of weight lifted from his shoulders. For a moment he felt light, almost floating. She did it. She'd fought back. She'd won. For today at least, he wasn't going to lose anyone.

He hadn't been there to see it, hadn't been there when she woke up, but that was okay. And he might still be infected, might yet find himself unconscious in a plastic tent with tiny robots attacking his brain, but that was okay too. Because she'd survived, she was going to live… and that made it all worthwhile.

TBC...