It was less than a day later before the situation John Sheppard had been fearing came to pass, and he was forced to face his nightmare. He'd spoken to Rodney McKay later the previous evening and all but ordered him to find a way to completely neutralise Elizabeth's nanites so she wouldn't have to be put into stasis or worse yet deactivated. On his way out of the science lab he'd bumped in Dr Zalenka and brusquely ordered him to double check the stasis chamber was ready to be powered up at a moments notice.

" But why?" Radek started to protest, his voice thick with his accent.

" Just do it" Sheppard snapped and stalked out of the lab, leaving too rather frazzled scientists in his wake. He'd taken himself for a run to drain the aggression from his body, his entire body screaming for a reprieve before he slowed his pace even a fraction. The city was bathed in darkness, suiting his mood and hiding his drawn features from the other members of the expedition. Soft lighting illuminated the sections of hallway and piers as he passed, returning to darkness as soon as he'd moved on, conserving power.

It had been in the wee hours of the morning that the city shuddered from the assault from space, lights dimming as power was routed away from non-essential systems and into the shields. John tumbled out of bed and was out the door even before he'd had a chance to lace his boots up properly, heading towards the control room to see what was going on.

He nearly ran into a pylon as the city shook from another hit, bracing himself with his arms before pushing off and continuing on his flight.

" What's going on?" He puffed as he skidded into the control room, the area a flurry of frenzied activity as key personnel struggled to keep up with the attack.

" It's a Replicator ship, we think they've picked up the signal from Elizabeth's nanites and are investigating" Carter explained, gripping a consol as the city shuddered again.

" Are you sure?" John asked, a sinking feeling in his gut. If the Replicator's had found Elizabeth, then he would be forced to.... no he wasn't going there just yet, there had to be an alternative.

" No.. but they're Replicators and they're here... 2 and 2 still equals 4" Rodney retorted angrily as his fingers danced over the keyboard of his laptop.

" Did you have a chance to look into Elizabeth's nanites?" John questioned, nailing Rodney with an accusing glare that made the stubborn scientist actually pale.

" No....but now I know why....If you get her into the stasis chamber it should neutralise any nanite activity" Rodney said quickly, his eyes wide with recognition. " We haven't tested the stasis chamber since... you know.. the other Elizabeth so I don't know if its working properly, and there's no time..." His words were cut off as the city shook violently again.

Dr Elizabeth Weir was nearly shaken out of bed as the city rocked beneath her, waking her up more efficiently than any strong coffee could. Quickly changing out of her night clothes and into her regular uniform she tugged on her boots and headed up to the control room out of habit, not realising she wasn't really required there anymore.

As she emerged in the control room an eerie silence fell over those gathered there, making her wonder what exactly was being heatedly discussed before her presence was noticed. Any words were cut off as John grabbed her wrist, pulling her back the way she'd come.

" Elizabeth... you've got to come with me. Have Zalenka meet us in the Stasis Room" He said stoically as he half jogged half ran down the corridor with her in tow. She saw Carter's face fall and Rodney's head in his hands as she turned.

" John, what's going on?" Elizabeth shouted over the din, the confusion on her face evident as she was half pulled half dragged through the corridor.

" We need to put you in stasis...the Replicators may be trying to find you" John replied, slowing his pace just a little as the corridor became crowded.

Realisation dawned on Elizabeth " You're trying to protect me...to protect yourselves" she started, gripped John as the city shuddered again.

" It's either this or Rodney tries the kill-switch again, and that's one option we are NOT exploring" John retorted angrily, picking up the pace again as the people thinned.

Within a few minutes they'd arrived at the stasis room, Dr Zalenka waiting anxiously for them as they entered. He looked disheartened by what he had to do, but knew there was no avoiding it. Elizabeth hesitated as she saw the chamber again, causing John to turn and release her wrist.

" Elizabeth… it's the only way" John insisted, not voicing the alternative again. Thankfully Radek had the nous not to voice his own concerns about the lack of testing and analysis on the stasis chamber. There was a naquedah generator attached to the controls in the centre of the room, quietly humming away as it provided a power source the Replicators couldn't take down with their weapons.

" Just in case the shields fail... or we lose power… this should keep the stasis chamber going long enough to someone to get down here and reanimate you" Radek explained quickly, his accent making it hard to understand the exact words.

" It's ok Radek..." Elizabeth said quietly, giving him a look that conveyed her acceptance. She always knew there would be an issue with the nanites if they were never completely neutralised. This was the price she would pay for the chance to live again. John released the grip he had on her wrist, his eyes speaking an apology that words could not explain. She simply nodded and stepped towards the chamber, wondering what it would feel like to be put into stasis.

" Everything seems ready" Radek lamented as though he wished there were another alternative.

" Elizabeth I...." John started, before a finger on his lips stopped him. The finger was replaced by a featherlike kiss, a kiss that promised more should the situation allow it. She broke the contact to see a very red faced and embarrassed Zalenka trying very hard to look anywhere but at the two of them. Without a word she stepped into the chamber and turned to face them, John's anguished face and Radek's sombre expression the last things she saw before the world faded to black around her.

" The system looks stable" Radek noted as he checked and rechecked the stasis chamber's systems. The naquedah generator supplemented the power source and was functioning efficiently, allowing him to breathe a small sigh of relief.

" Nanite transmissions falling….. " Rodney's voice echoed around the quiet chamber as he patched himself through the communications system into the room.

" Thank God" Radek sagged in relief, relinquishing his death grip on the controls. John had vanished to the chair room as soon as Elizabeth was 'secure', leaving Radek feeling very much alone.

It took a short time but the weapons fire seemed to slow as well, as though the Replicators were trying to figure out why the transmissions stopped. They lingered for several hours longer, taking the occasional pot-shot before leaving the area entirely, allowing everyone in the city to relax finally.

John emerged from the chair room looking drained both emotionally and physically, his complexion pale in comparison to the shock of black untameable hair he sported. He made his way to the control room to see Carter in deep discussion with McKay, neither looking very pleased with whatever it was they were talking about.

" We can't keep her in there forever" Rodney was protesting, his hands animating his frustration.

" We can't let her out with the nanites still transmitting… It'll bring the Replicators back here in a heartbeat" Carter implored, her expression sympathetic but firm.

" I….. I just need some time to figure something out" Rodney stuttered, his hands already beginning to tap away at his laptop.

John caught the tail end of the discussion and motioned Carter towards Elizabeth's old office. She nodded towards McKay and left him to work.

Once the doors closed behind them John couldn't hold his anger back any longer.

" You're planning on leaving her in there aren't you?" He exploded, his tone the barest inkling away from insubordination.

Carter sucked in a deep breath as though she had been expecting this confrontation, schooling any irritation away from her features and keeping her expression neutral.

" I plan on keeping her in stasis until McKay can permanently disable her nanites… yes." Sam explained carefully, hoping that Sheppard would see her point of view.

" Was that the plan all along?" John accused, his face dark with anger.

" No. It wasn't until the Replicators arrived to check out the nanite transmission did we realise the gravity of the situation. The dampening field obviously hadn't worked like we'd hoped. When Rodney works out a way to neutralise that transmission and the nanites for good, she'll be released. Not before. We can't risk it" Carter plonked herself behind her desk and regarded John with a commanding gaze. She understood his frustration, heck she felt it herself, but the wellbeing of the city and the expedition was her primary concern just as it had been Elizabeth's. The needs of the many had to outweigh the needs of the one.

" I know why you did it, I just don't like it" John finally calmed, his expression changing from one of anger to one of resignation.

" I understand John, but it's up to the scientists now. As soon as they can sort out the nanites, everything will be resolved. Until then... she stays in stasis." Sam finished, putting an end to the discussion and any rebuttal John may have been thinking of.

He hesitated a few moments before a crisp " Yes Ma'am" and stalking out of her office.

Much to his chagrin the repairs to the city kept him occupied for a number of hours, it also gave the scientists a small headstart before he could start nagging them for progress. After a drive-by the science labs to check on their progress later that evening John finally ended up in the stasis chamber, his feet having had a mind of their own and taken him there as his mind stewed over the possibilities of never seeing Elizabeth alive again.

She looked so peaceful encased within the stasis chamber, her eyes gently closed and the glass slightly opaque to indicate the chamber was indeed working. John's heart clenched in anguish, seeing her so peaceful and so close, yet so untouchable.

How long would she be forced to remain like that? His hand reached to touch the glass, the fingertips tracing the line of her jaw through the frosted material. He felt so terribly alone in the universe at that moment, cut off from the one person he drew strength and courage from. Could he go through losing her a second time?