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They didn't all die. Luckily, despite his gruff tone, Caldwell did seem to believe them, at least enough to send a security team down with scanners rather than risk destroying Atlantis and murdering them all. His decision to overlook the standing orders and not vaporize them all made Kai think better of Caldwell, just a little.

Once the marines were in the gate room they came forward with guns raised. Their small group, John, Kai, Elizabeth, Rodney, Teyla, Ronon, Woolsey and O'Neill, all stood in a line, trying not to look intimidating. Which, even without their weapons, some of them managed to accomplish better than others.

The military personnel all repeated their authorization codes but eventually it was O'Neill's impatience and snark that made the marines report back that all seemed well. The marines were beamed back to the Daedalus. Beckett assured Caldwell he would be running full tests on all of them to make sure there was no chance any of them had been infected. Caldwell thanked him, and told them he and his crew were going to get some rest while they waited for the results. The crew of the Daedalus had been running full out to get to Atlantis as quickly as possible.

Once the marines beamed back to the Daedalus. The control room was eerily quiet and empty. The only sound was the gentle hum of machinery in the control room. The level of exhaustion in the room was almost palpable.

"Not vaporized," Woolsey said breathing a sigh of relief and hanging his head. It was clear to everyone there the poor man wasn't used to coping with this level of stress in his life.

"Not today," John said brightly, although his eyes were tired.

Elizabeth turned to face O'Neill. "So what's next?" She asked. Those who knew her, could see the tightness around her eyes as she asked the question. They had beaten the Replicators, but to do so they had gone against orders. There would be consequences. Elizabeth glanced at John. The Colonel had never worried about going against orders when he believed it was the right thing to do, but she was not so sanguine. She knew the IOA, they were not likely to forgive and forget.

O'Neill crossed his arms and rocked back on his heels in his good 'ole boy act. "Well I was thinking home, a hot shower followed by a hot toddy-"

"That's not what I meant," Elizabeth said, cutting him off a little more sharply than she probably should have in front of so many subordinates. But she couldn't leave this alone. Looking back at the tired, worn faces of their team she had to get them answers. They had risked so much to save their home and they deserved to know if their efforts were in vain.

The goofy smile fell from O'Neill's face and he suddenly looked just as tired as the rest of them. "Look, Elizabeth, if it were up to me-" O'Neill started to say seriously.

"It is, up to you," Elizabeth interrupted again.

O'Neill smiled wryly as though it had just occurred to him that he actually was the man in charge. "Right...well, you'll probably still need the rubber stamp from the IOA, but you can all stay. Welcome home," he said with a pleased smile.

Elizabeth threw her arms around O"Neill's neck impulsively. He patted her back uncomfortably and side stepped out of her reach after the minimum amount of time that was polite.

"Well done everyone," he said looking over the group. "Although next time, consider bringing Carter with you," he said with a fond gleam in his eye. "Well, I think once we get our scans from the good doctor we could all use some shut eye."

The others nodded and dutifully turned to face Beckett, waiting for him to take charge.

Kai glanced over the group and stepped up to O'Neill. She nodded once respectfully. "I would like to request gate travel to return to New Athos as soon as possible."

John looked like someone had hit him. He stopped mid stride and glanced back. Kai was pointedly not looking at him, but everyone else was watching him, waiting for his reaction. He swallowed and fought to keep his face blank.

O'Neill saw Sheppard's expression over Kai's shoulder before he responded. "Sure, but probably later," O'Neill said with a casual wave of his hand. "I have a meeting with Woolsey and we need to be sure none of us have an tiny robots in our blood streams before we make any official decisions about leaving."

Kai set her jaw. He had literally just made the decision to allow Weir and Sheppard to retake control of Atlantis regardless of what the IOA thought. He could absolutely make the decision to let her dial out. She turned to look over her shoulder, wondering if Sheppard somehow had something to do with this.

"Kai dear," Beckett called, catching her attention. "If you'd like, I'll start with you," he offered. Beckett didn't want to see Kai leave, but he had seen the hurt in her eyes and he wouldn't make her stay if she didn't want to. She belonged here, he absolutely believed that, but she needed to believe it.

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The scans took a surprisingly short amount of time. It took longer for Beckett to figure out where the Replicators put all of his equipment when they repurposed the infirmary than for Kai to lay on the med bay bed and hold still for the can. The green light ran up and down her body and then beeped.

"Right," Beckett said. "There you are dear. I'll have the results back by morning."

Kai frowned. "Morning?" she clarified. She couldn't seem to remember it ever taking that long to get Replicator scan results back.

"Aye," Carson said. "Unfortunately, none of my equipment is set up," he said gesturing to the room around them. The scanner beeped, he looked down at it and pressed a button, wiping it clear. "Those scamps," he said with an exaggerated shake of his head.

Kai narrowed her eyes suspiciously at Beckett. She had never once heard him refer to Replicators as 'scamps'. "Please inform me as soon as you have the results."

Beckett's eyes were wide and innocent. "Of course dear, I would never keep something like that from a patient."

Kai signed and climbed to her feet. She wasn't familiar enough with the scanners to know for certain that he was purposefully taking longer than necessary. Although when Weir had been infected with nanites she remembered the scans being instantaneous.

"Sleep well," Beckett called after Kai as she stalked out of the infirmary.

She turned the corner to head back to the control room and froze as she came face to face with John. He had been leaning against the wall, clearly waiting for her. She glanced back over her shoulder, but there was no other way out of the infirmary and no way for her to avoid him.

"Kai," he said, pushing off the wall.

Kai felt a distant pulse through the Bond and made both of them flinch in pain as she fought to close the Bond even tighter. This close to John however, it was all but useless.

John grimaced and dropped his head as he fought against the tight pain in his chest. "You don't have to do that," John said, his hand resting over the middle of his chest.

"What do you want?" Kai asked cooly, ignoring his statement. She absolutely did have to keep them separated. She couldn't let the Bond open any further. He had made it clear he had come to her for assistance in saving Atlantis. They had accomplished that task. It was time for her to move on.

It was painful for John to see Kai so closed off. Her face was an expressionless mask of carefully contained emotion. But he knew her, knew she was either hurt or angry or both. He hated that she was fighting so hard to cut him off. Hated that she looked as she had when she first arrived on Atlantis with hard suspicion in her grey eyes. Hated that it was his fault.

He took a step towards her and she actually took a step back, keeping the physical distance between them as though he would hurt her somehow. His gut churned. 

"Kai," he said her name and her eyes hardened.Clearly he was going about this the wrong way. "Are you really going to leave?" he asked, looking down. He glanced back up at her just in time to see her reaction.

Kai's eyes flared at his choice of words, but she contained her desire to shout and rail at him. He was accusing her of leaving? "Our mission is completed," she said instead of all she wanted to say.

"Kai," he said her name again but this time it was full of all the emotion and things he didn't know how to say. John had never been good at talking about his emotions. Every single one of his exes would have agreed. But it mattered now. The Bond had always made things so easy between them, but with Kai fighting it, he had to say something, anything to keep her from leaving. "Don't go," he finally settled on, mirroring the words he had spoken so long ago when things were still new between them.

Kai flinched like he had struck her. The last time John said those words they had been in the jumper bay and she was getting ready to leave. The Mortii assassin had found her and she was running. It was their first real kiss. They had kissed before that, when the creature had control of John, but that was the first time they both had done so with their eyes open and honest about their feelings for one another. John had asked her to stay, to trust him that they could handle it. In the end, she had chosen to stay, and chosen to trust him. Her mistake.

Without another word, she side stepped around him as she all but fled down the hall. She went to turn the next corner and rocked back on her heels as she nearly collided with O'Neill.

"Whoa," he said holding his hands up in surrender.

Kai had a moment to wonder if the Colonel had heard her and John fighting. Honestly though, it didn't matter anymore. She wouldn't be here much longer.

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Kai stood out on a balcony overlooking the water. Some of the others had gone to get some sleep in their quarters, but she wasn't going to stay here a minute longer than she had to. She had done her part, Atlantis and her friends were safe from the Replicators. She could move on.

The door slid open behind her and she turned with a surprised frown when she heard General O'Neill step out. She had been expecting Sheppard to come fight with her some more, it disgusted her to realize she was a little disappointed.

O'Neill didn't say anything, instead he moved over to the railing beside her and gazed out at the water.

With a frown, she followed his lead, resuming her quiet contemplation. She had no idea what business he had here. They two of them had never spoke before, not really. He had spoken around her, but he had never really taken an interest in her.

"So, you want to leave, huh?" O'Neill asked after a beat.

"I would not have asked if I did not," Kai replied stiffly. She did not owe this man an explanation. She had a natural distrust of authority and as far as she could tell, he held the highest rank of anyone from earth she had ever met.

"I only asked because it kind of seems like you like it here," he said gesturing around them to encompass the city. "I mean why else come back and risk your life fighting for it?"

Kai followed his gaze to take in the ancient city. It somehow felt peaceful here. Despite all the battles and blood that had been spilt to protect it.

"It was the first home I ever knew," Kai said, almost surprised to find herself speaking her truth to the General. She did not owe him an explanation.

"So why give it up?" O'Neill asked conversationally.

"I don't belong here anymore...Why am I even talking to you about this?" She found herself asking aloud. She turned and scowled at the General.

A smile flashed in O'Neill's eyes. "I've just got one of those faces," he said with a shrug.

"I need to find my place in the Galaxy," she said decidedly.

"Kinda seems like you have a place here," O'Neill pointed out.

"I need to leave," she said decisively.

"Does you needing to leave have something to do with that fraternizing report I received from Weir a while back."

Kai's eyes snapped with temper. "The Colonel and I did nothing wrong," she said resolutely. "I am not his subordinate, I am not a member of the U.S. military and it did not effect either of our performances here."

"Is this it not effecting you?" O'Neill clarified sardonically.

Kai narrowed her eyes for a second and wondered exactly how much trouble she would get in for punching a General.

"Look," O'Neill said changing the subject before Kai could act on whatever thought had that dangerous gleam in her eye. "I don't really know what's going on here. Obviously, something has Sheppard in there looking like someone kicked his puppy," he said gesturing over his shoulder. "And it was hard to miss whatever was going on in the hallway, but the truth is they need you. It's going to be a while before we can round up enough people to keep this place running and I hear you're pretty good with the systems." O'Neill shoved himself away from the railing and headed back towards the door.

"I didn't agree," Kai called after him.

"Oh I know," O'Neill said turning back around with a grin. "But those results won't be in until morning. You might as well get some sleep and think about it."

"Why would you want me to stay after the big deal you made about Sheppard and I?" Kai challenged.

"Who me?" O'Neill asked. "I never cared you were together. Sheppard needed to work on keeping his temper when it came to protecting you though. He loses it on the wrong person and well...not good for his career. I was helping," he said with a smile. "See, the way I see it, you can't always control who you fall in love with. But just because they tell you not to, doesn't mean you shouldn't."

The door slid shut behind O'Neill and Kai breathed out a frustrated sigh. The General didn't know what he was talking about, he didn't have all the information. He was right about somethings though. Atlantis would be difficult for their small group to run until they were able to get the rest of the personnel back. Assuming they even could. Four weeks was a long time. It would be a tall order to find enough people without previous commitments to staff the city. Kai could stay long enough to help keep things running, she supposed.

Kai shoved herself away from the railing and went back inside. Elizabeth looked up from where she was sitting in her office. Elizabeth's look was questioning and Kai just nodded. Elizabeth smiled gently looking relieved. Kai went to the transporter and headed towards her old quarters.

The room was empty of even the few personal touches she had before, but it still felt like home. She pulled off her belt, laying it and her Blades on top of her dresser. She unwound her headscarf and carefully folded it. It was still the same midnight blue scarf John had gotten her after losing hers to the Wraith planet.

Kai lay down in her bed and stared up at the ceiling, listening the the crush of the waves below the tower. She closed her eyes and felt a shift in the Bond. She was close enough to sleep she didn't have to energy to shut him out. Instead, she let herself relax into the security of the Bond. Kai wasn't eager to revisit the empty desolation she had experienced in the absence of the Bond which had robbed her of sleep all those weeks.

Kai was torn. It felt weak to stay, but it also felt weak to run away. She wondered when and how her life had become so complicated. John Sheppard was of course the answer to that. But she wouldn't let him stand in the way of helping her friends. O'Neill was right. She did like it here, it was her home and she had a place. Atlantis was a big place, she could keep the Bond closed and keep herself separated from John. She almost believed the lie herself.

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John couldn't allow himself to sleep, no matter how tired he was after Beckett completed the scan. John was the last of the group to be scanned. All the others had gone off to bed.

As soon as the machine beeped Carson looked down at the reading
"You're clear," he informed The Colonel.

"Thanks doc," John said climbing to his feet.

"Colonel," Beckett said gently. "About Kai..."

John exhaled. He knew his friend was just trying to help, but he didn't need yet another person pointing out all the ways he had screwed up. He was well aware he had failed to say the right thing, over and over again. Kai had allowed herself to trust him and be vulnerable with him and he had botched it all terribly.

"What about her?" John asked a little tightly.

"Don't give up," Beckett told him.

John opened his mouth and closed it, unsure how to respond to Beckett's heartfelt words. He had always viewed Beckett as something of a romantic and he had always been kind to him and Kai, quietly cheering for them even before they had admitted how they felt about one another.

"Not planning on it," John assured him, turning towards the door.

"I just mean..." Beckett started and stopped himself.

"What?" John asked.

"She doesn't know how to trust Colonel. Her trust and loyalty has always been fragile."

"You think I don't know that?" John bit out the words bitterly. He wasn't upset with Carson, not really. He was pissed at himself.

"I don't doubt you know that, just...be patient with her and perhaps...perhaps you'll find she'll be patient with you."

John snorted doubtfully and shook his head. "Thanks Carson, I'll keep that in mind," he said and he headed down the hall towards the control room.

He was surprised when he didn't find her on the balcony overlooking the waves. He would have sworn she would have stayed out there. He went back inside and saw Elizabeth in her office.

He nodded to her and turned to try the lab.

"She went up to the living quarters I believe," Elizabeth called after him.

John hesitated but moved to the transporter. When he came out he hesitated, instead of going to her quarters he went to his own. As badly as he wanted to confront her again, and force her to listen to him, he recognized that she would still be there in the morning. For now anyway, she was staying, that was a victory in itself.

He lay down in his bed and closed his eyes. Deep in his chest he felt a small shift. It wasn't exactly the Bond opening, more like settling. He rested his hand over his heart, where he could feel her and drifted off to sleep.

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