The city shuddered beneath John's feet as he sprinted towards the infirmary, a trail of medics and military personnel on his tail as he ran. It took far to long in his opinion to get there and as he did he laid Elizabeth out on the first available bed whilst Dr Keller hurried to get the scanner hooked up and in position.

" Carter to Sheppard, the shield's weakening, looks like they're adapting, I don't know how long its gonna last" Her voice was calm but conveyed a sense of urgency John had rarely heard from her before. So much was riding on Elizabeth, for an instant he thought it may be too much.

The scanner hummed to live, descending slowly along Elizabeth's body and displaying the detailed images on a nearby computer screen. Slowly but surely the Nanites within Elizabeth's body were rebuilding her brain as well as the other parts of her body they had used themselves to repair previously, this time they were creating organic components, components that couldn't be harmed by the virus that would kick in at any tick of the clock.

" How is she Doc?" Sheppard asked anxiously, hating the fact that seeing Elizabeth pale and unconscious reminded him of when the nanites tried to overtake her body the first time around. How long ago had that been now? It felt like a lifetime but he pinned the exact number to the day in his mind. If this worked, he would have Elizabeth back as whole as she had been before Niam had attacked her. Still, he couldn't get his hopes up just yet, they'd been dashed before.

" The nanites are rebuilding her brain as we speak, it'll take some time before she's conscious though" Keller announced from her position in front of the monitor. She looked at another monitor which displayed Elizabeth's vital signs, they fluctuated as her body dealt with the changes being made, her blood pressure and neural activity spiking periodically.

The next blast nearly through them off their feet, the impact far worse than anything they had felt so far. The shield had been breached and soon Replicators would flood the city in their search for Elizabeth.

" Shields have collapsed, all personnel report to defensive positions" Carter's clear voice rang through the corridors, causing a stir of activity. Weapons were drawn and checked, scientists barricaded themselves in their labs, and the infirmary prepared itself to the usual inundation of patients that usually came from the cities defences being breached. John however stepped forward.

" Clear the room of all but essential personnel, set up your triage in the Mess Hall" he ordered, causing a worried look from Keller.

" We can't just up and leave, there are patients here who need…" She started, only to be cut off by Colonel Sheppard.

" They're here for Elizabeth, the more people in the way, the more people get hurt" John replied, his tone low and lethal.

" Sam, the way to get out of this with the least amount of bloodshed is to let them into the city, and clear a path to the Infirmary, they're after Elizabeth first up" John explained through his earpiece to Sam, who clung to her consol as the city trembled beneath her feet.

" Are you saying we LET them have her?" Sam questioned, her tone uncertain as chaos reigned supreme in the control room.

" It's the only way to get out of this with the city and most of us intact" John replied quickly, steadying himself on Elizabeth's bed as the deck bucked.

" Alright… I hope you're right on this John" Sam signed off and sent another announcement through the military personnel's com pieces advising them of the change. They were not to approach the Replicators unless they were directly being threatened.

Before long a small army of Replicators emerged into the corridors of Atlantis, only to find the majority of the expedition nowhere to be seen, or if they were around, non-confrontational. It didn't take them long to narrow the location of the one who had escaped and to close in her position.

Sickbay was all but deserted when the small number of Replicators cautiously entered, carefully looking for any traps or hidden attacks that might be sprung upon them. John stood alone beside Elizabeth, his ARG lowered but his finger still on the trigger.

" We have come for her" The lead Replicator announced without emotion.

" I know" John replied, his weapon still lowered.

They advanced until the lead Replicator was level with Elizabeth's bed, opposite John and regarding them both carefully. This lack of confrontation confused them greatly, they had anticipated much resistance.

His hand raised and approached Elizabeth's forehead, causing John to raise his weapon.

" I won't let you take her" He threatened, his voice barely above a whisper in the silence.

" She is one of us, and will be returned to us" The Replicator intoned, as though he were explaining the complexities of the colour grey to someone who was colourblind.

" Like hell she will be" John retorted, his finger itching to pull the trigger. He knew at this critical juncture the Replicators mustn't catch on to the ruse, if they did, all would be lost. He deliberately stepped forward in front of the nearest Replicator, a stupid move that no military officer worth his stripes would ever do but knowing he had to keep the ruse going. As predicted they retaliated, sending him reeling into the bed next to Elizabeth's. The impact left him groggy and disorientated, unable to control his own movements as the sound of screaming hammered his ears.

Not just any screaming… Elizabeth's.

He cracked open an eye to see her writhing on the bed, the Replicator's hand deeply embedded within her forehead. They were probing her mind, trying to learn what she had accomplished since they had noticed she was missing.

The look of shock crossed their faces simultaneously, followed by the inevitable look of defeat as the virus was uploaded into their bodies. A moment later they all fell into a pile of silver dust on the floor, the sound not unlike the raining of marbles from a small height.

Dr Keller emerged from behind one of the patient partitions, a look of fear mixed with relief on her face. She tentatively made her way to Elizabeth's side, checking the other woman's vitals whilst trying not to step in the pile of dust that was the Replicators.

John groaned from his uncomfortable position, slowly regaining control of his mind and muscles. He pulled himself upright and leant on the bed for support.

" Is she ok?" He asked, his voice thick with concern.

" She appears to be, the nanites have finished repairing her brain and uncoupled, they're still in her bloodstream but now 100% inert. It'll probably take her a while to get back to normal though, she's been through a lot" Keller explained, having finished with Elizabeth and making her way over to John. " How are you doing?"

" Next question" He grumbled, struggling to hoist himself back onto the bed. Truth be told he hurt like hell and the blood curdling scream still echoed in his ears.

Keller gently pushed him back onto the bed, unzipping his tactical vest and pushing it aside to better examine his torso. From what she could see he was badly winded and would be sporting a large bruise for some time, but was otherwise relatively uninjured.

The next two days for John were spent in the Infirmary, mostly in a chair pulled up by Elizabeth's bed once he was released from his own by Keller. Everyone came to visit, even Rodney who stood there in a rather awkward silence until his brilliant mind tried to form some kind of sympathetic coherent thought.

Elizabeth thought she was alone when consciousness finally decided to grace her with its presence. She could hear the muted shuffling of the medical staff nearby, coupled with the steady rhythm of a heart rate monitor. A slight pressure on her index finger signified a blood oxygen monitor as well, it was cumbersome as she tried to experimentally wiggle her fingers, remembering the sensation from what seemed like so long ago.

" Hey…good to see you awake" Came the quiet voice of Jennifer Keller, glancing from Elizabeth to the monitors that were displaying her vital signs. Elizabeth cracked open her eyes and blinked to clear the fuzziness from them. Her gaze fell upon a shaggy mop of untameable black hair buried in the crook of a black clad arm, obviously asleep.

" Has he…?" Elizabeth asked, already knowing the answer to her question.

" No, he hasn't moved, and its good to see him finally getting some rest, although its not the most ergonomically sound position" Keller said gently, keeping her voice down so as to not disturb John. Elizabeth however had other ideas, raising a weak arm to gently ruffle his hair, a tender touch with more meaning than either would care to admit. John's head snapped up at the contact, his eyes confused for a moment before taking in the very much alive and awake woman before him.

" You're awake…" He stated groggily as his mind cleared itself from the lingering fog of sleep.

" It seems that way " Elizabeth remarked, holding the contact with his eyes as long as she could without seeming overly obvious. " Mind filling in the gaps? I'm still a little confused how I got here…"

John sucked in a breath before leaning back in his chair. " Do you remember being put into stasis?" He questioned.

" Yeah, feels like yesterday" She replied, rubbing her forehead with the hand not attached to any IV lines or monitoring equipment.

" It was months ago. It took Rodney that long to come up with a way to get rid of those nanites inside you once and for all, as well as coming up with a rather genius plan – even by my standards – to take out the Replicators for good." John started, pausing for a moment for Elizabeth to digest the information.

" Problem was, the Replicators were looking for you, and keep attacking the city trying to find you. To get this plan to work we had to take you out of stasis, reprogram your nanites, then use you as a lure to bring them here. They tried to probe your mind and got infected with the virus Rodney created, and Bingo, no more Replicators" he finished, making a point not to mention the sight of her writhing in agony or the way her screams would stay with him for the rest of his life.

" I see" Elizabeth said simply, processing the information at her own pace. She would ask him more later when she didn't feel like she would fall asleep on the spot. She rested her head back on the pillows, her eyes closing of their own accord as her energy reserves bottomed out.

Dr Keller checked her vitals again to find her resting this time, falling gently into a deep healing sleep. She saw the question in John's eyes " She's just sleeping, it'll take a while before she's back on her feet" She put his mind at ease. " And you should get some sleep too, the next bed's free if you want to crash out there"

" Yes Boss" he grumbled, easing himself out of the chair and hoisting himself on the bed, unlacing his boots and pulling off his vest before curling up on the bed, instantly asleep.

A week later Elizabeth was finally released from the Infirmary, given a clean bill of health and completely free from nanites. A innovative therapy devised by Rodney and Dr Keller had removed the inert nanites from her bloodstream, not that she was awake enough to know how they did it. That week had been spent in a haze of semi-conscious sleep and increasing amount of alertness. John had filled in most of the gaps in her memory and she revelled in the fact that she had played a rather substantial roll in ridding the galaxy of one of its scourges. Not that the victory would last long, they never did in the Pegasus Galaxy.

The next day she was summonsed to Carter's office… 'her old office' she mused to herself as she dressed in casual clothes that morning. John had given her breakfast in bed before leaving to go about his duties, letting Elizabeth get ready in her own time. She could sense something was going on but no-one was letting on, going about their business with an oddly familiar look on their faces.

She knocked on the doorframe of her old office and saw Sam's head rise from the report she was engrossed in.

" Dr Weir, it's good to see you up and about" Carter said pleasantly, gesturing to a vacant chair on the opposite of her desk. Elizabeth plonked herself in the offered chair, realising how weird it felt to be sitting on this side of the table.

" You wanted to see me?" She asked, rising an eyebrow at Sam's small mountain of reports awaiting approval.

" I did… I've informed the IOA of your progress and recovery" Sam started without preamble. Interlacing her fingers and setting her hands on the table.

" I see" Elizabeth replied, not sure where Sam was going with this rather abrupt start to the conversation.

" They want you back as leader of Atlantis, when you're ready to take it on again, I'm apparently needed more back on Earth" Carter explained, obviously not happy with the whole idea. Atlantis was the dream posting of any miliary or civilian personnel, and it hurt to be recalled away from it at such short notice. " There's a catch though, Mr Woolsey will be here as an overseer for the first 6 months, just to make sure you're still as he put it 'Right for the job' "

Elizabeth stayed silent for a moment, unable to come to terms with the fact that she was once again put back in charge of such an expedition. The glory was tempered with the bittersweet though of Woolsey being a constant thorn in her side for the next six months.

" I'm sorry to hear you've been recalled to Earth, from what I hear you have done a wonderful job here" Elizabeth said diplomatically, nodding her head towards Sam in a gesture of respect.

" I did what I could, I can't say it was ever easy" Sam replied, leaning back in her chair. The silence seemed to engulf them as they each got caught up in their thoughts.

" I'm sorry, I shouldn't keep you from your work" Elizabeth stood, ready to excuse herself from the office that would soon be hers.

" Think nothing of it, I needed the break." Sam rubbed her eyes with the back of her hand. She looked tired, as though the last several months had taken their toll on her. She had proven herself here on Atlantis as a strong and capable leader, but as she had admitted, it hadn't been easy. "Congratulations Dr Weir" Sam extended her hand.

" Thank you, and thanks for keeping this place in one piece, its not a mean feat these days" Elizabeth quipped, shacking Sam's hand before letting herself out of the office.

Her feet took her to her favourite balcony as her mind processing the good news, she leant against the railing, enjoying the feel of the breeze in her hair and the scent of salt in the air. Inhaling deeply she closed her eyes and savoured the sensation, wondering how quickly she had forgotten the peace and tranquillity this balcony had always provided.

" I see Carter told you the news?" A voice came from behind her, and she grinned in reaction.

" You knew" She stated simply, twisting to see him emerging from behind one of the pillars with a lopsided grin on his face.

" It was hell keeping it from you, but Carter wanted it to be a surprise" John remarked, settling in behind her and wrapping his arms around her protectively.

"So that's why Rodney's been grinning like an idiot for the last two days" Elizabeth quipped, resting her head back against the strong chest behind her.

"That would be it, poor Rodney's never been good with secrets, but I must admit its remarkable what the threat of slipping a lemon into all the food in the galley can accomplish" He smirked, giving her a little squeeze to prove his point of victory.

Elizabeth bit back a retort but decided against it, sometimes it was good to see the brilliant scientist taken down a peg or two. She enjoyed the warmth of John's body pressed against hers, the breeze still ruffling her hair and his chin now resting on her shoulder.

" This is nice" She sighed in contentment, laying her hands over his as they encircled her waist.

" It is, its nice to have you back, for good this time. I've missed you so much" John admitted, the level of sentiment unusual even from him.

" It's good to be back" Elizabeth whispered, giving his hands a squeeze.

For once, the Pegasus Galaxy seemed to be giving them a break for a change. How long it would last, no-one knew, but right at that instant, she was the happiest woman in the galaxy, nestled in the arms of the happiest man.

The End