I have to say I am beyond excited for this update! It has always been one of my favorite episodes and from the very beginning of writing Kai and John's story I always imagined how this episode in particular would play out for them and what it would mean for their relationship. I hope you enjoy reading it as much as I enjoyed writing it!

Happy Reading!

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The Long Goodbye
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Kai and Zelenka were just putting the finishing touches on the changes to the sensors. On the next system update the changes would go into effect and Atlantis would be capable of picking up any Mortii ships that entered the quadrant, whether they were cloaked or not. She was finished. It was time to go.

"Doctor Weir," Zelenka said into his radio. "The changes to the sensors are complete."

There was a long pause. "Understood Radek," Weir said and Kai thought perhaps the leader of Atlantis sounded a bit sad.

Now that it was done, Kai was at a loss for what to do with herself. She was just packing away her tools when word came in about new technology AR-1 had brought in from their last mission. McKay put out a request for Zelenka's team to come in to assist on the project. Radek had looked at her expectantly as he turned to head down to the lab assuming she would be joining him on their next project. No one but Weir and Sheppard knew of her plans to leave and she didn't have the heart to break it to Radek now. She was a coward. So, Kai packed up her tools and trailed after him.

She and Zelenka met McKay and Beckett in one of the quarantine labs on the east pier. It seemed they had found what appeared to be an alien pod in orbit around a planet with a single life sign inside and they were determined to revive the occupant. The excitement in the lab was almost a tangible thing.

"Have you seen anything like it?" McKay asked her as soon as she stepped through the door.

It was the size of a life pod but Kai didn't recognize the technology. "No, never," she replied after a minute. She scanned it and tapped on her tablet but nothing she was reading implied there were any sort of defense systems that would hurt anyone who tried to open it.

Sheppard swaggered in the door. He pulled up in surprise when he saw Kai working on the pod. They hadn't spoken since they came back their ordeal in The Tower. Kai had thrown herself into her work and Weir had contacted him as soon as he got back that she had finished the changes to the sensors. Which meant her time was up, and she would be leaving. He had been crabby since, now he didn't know what to think.

He pressed his lips into a grim line and turned his attention to McKay pointedly ignoring Zian. He and Kai had been civil on the mission but the tension between them was still there since he had yelled at her in the jumper about leaving. He didn't regret what he said, but he also didn't know how to make things better. If she was leaving anyway it didn't much matter what she thought of him. It was probably easier for her to be mad at him. 

McKay was too engrossed in his work to notice, but both Beckett and Zelenka picked up on the tension immediately. The two men shared confused looks, but when neither Kai nor Sheppard acknowledged one another they focused on their own work.

Doctor Weir and Colonel Caldwell stepped into the room behind Sheppard. "Doctor Weir," Beckett greeted. His eyes widened in surprise. "Colonel Caldwell, welcome back."

"Thank you Doctor," he looked up and met Sheppard's gaze. "Colonel," he greeted with a nod.

Sheppard nodded back but the tension in the room that had been bubbling between Kai and Sheppard seemed to have shifted into something else now that everyone in the room was watching Caldwell like he might attack someone without notice. This was his first trip back to Atlantis after the incident with the Goa'uld.

"What do we got?" Caldwell asked with interest.

"It's a life pod of some kind," John said crossing his arms over his chest.

"It appears to have been designed for the sole purpose of maintaining a single human life in stasis. This one is a female," Beckett said as he bustled around the pod double checking his readings. His whole focus was one the life inside the pod while Zalenka, Kai and McKay were monitoring the technology.

"There's another one in a decaying orbit, but ah, we could only fit the one in the jumper," John explained.

Weir stepped up next to the pod. "I've already sent Lorne and his team to retrieve the second pod. Ronon and Teyla are with them."

McKay popped up from underneath the pod, his tablet cradled in his arm. "Okay, we're ready to crack her open," he pulled up in surprise when he saw Caldwell. His eyes flickered to Sheppard, who still seemed uncomfortable but wasn't upset by his presence. "Hey," he greeted awkwardly.

"Hello Doctor."

McKay activated the pod and the door slid open to reveal a very old woman. She was wearing what looked like a flight suit.

Beckett checked his instruments. "She's alive, barely...I believe we found her very near the end. All the major organs are shutting down."

"How long was she out there?" Weir asked, shaking her head in disbelief.

"There's no way to tell for certain."

Kai was working her way through the pods main computer but couldn't find a date of execution of the pod. Which didn't seem likely. Anyone who would retrieve the pod would need information about what happened. It was a huge design flaw to not have the information available.

"So she could be an ancient," Elizabeth said excitedly.

"Ah, the pod design makes me doubt that," McKay said. "Kai are you finding any information?"

"No...nothing."

McKay stepped up next to her, practically shoving her out of the way. "Let me check," he ordered. Kai quickly stepped aside, nearly tripping to get out of his way. She almost crashed into Sheppard. He reached out to steady her and snatched his hands back at the last moment. They met each others gaze and turned away from each other.

"There's no information here," McKay said, disgruntled.

"As I said," Kai replied with a nod.

Sheppard's eyes flickered to her once more, but he didn't react with his typical smile. He clenched his jaw as he looked back at the pod.

"It's a shame she can't speak with us," Weir said sadly. She took a step closer to the pod so she was standing directly over the woman. "Just imagine what she could tell us about her people and what happened to her," she added taking another step closer.

There was a blast of white light that caught Weir straight in the face. Her whole body went rigid and collapsed back, unconscious.

"Elizabeth!" John called and he and Caldwell caught her before she could hit the floor. They carefully lowered her to the floor.

"We need a medical team stat!" Beckett yelled and jogged over to their side of the pod and began working over Elizabeth.

"What the hell was that?" McKay asked sharply.

Kai frowned, her fingers skittering over her laptop as she re-read the analysis. "Some kind of data burst," she said. "I have no idea where it came from," she said looking up gravely.

The medical team showed up and put Elizabeth on the gurney, wheeling her off towards the medical lab. Everyone followed behind except Kai and Zelenka. There wasn't anything for them to do but figure out what went wrong.

Lorne's team arrived with the second pod a short time later. Kai directed them where to put it and cleared the room. She immediately began getting it hooked up to other sensors so they could monitor it for any more data bursts. When the pod appeared to be dormant she made her way up to the infirmary to check on Weir and find out what McKay wanted to do with it.

She walked around the corner to see McKay and Sheppard talking with their heads near one another. "This is not my fault," McKay said adamantly.

"We were all there, relax," Sheppard assured McKay offhandedly. He glanced up as Kai appeared. He swallowed and cleared his throat straightening. "Zian," he greeted with a brisk nod.

"The other pod is being monitored, so far it has been dormant," she reported.

Sheppard shifted his weight. "I thought you had finished up those sensors," he couldn't help saying. "Why are you working on this project?" he asked, not able to keep the accusatory tone in check.

McKay looked back and forth between them, completely obtuse as to what was going on between them. "Because she finally finished with the sensor project," McKay said as though it were obvious.

Kai cleared her throat, shooting Sheppard a pointed look. "I had the time," she replied tightly. No one else knew she was going and she didn't want Sheppard revealing her secret, not now. There was too much going on.

"Well, no need to do us any favors," Sheppard grumbled.

"It's no trouble," Kai responded through gritted teeth.

McKay frowned and looked back and forth between Kai and Sheppard, not fully understanding why they both seemed so snippy at one another.

"You-" Sheppard began but Beckett cut them off.

"She's coming 'round," Beckett called distracting Sheppard and Kai.

Everyone stepped up to the bed as Elizabeth's eyes fluttered open. She looked at everyone standing around her warily. She sat up slowly and held her body in a strangely rigid posture. Her eyes landed on Kai's scarf which was wrapped around her head and she frowned. Then her eyes flickered to the other people in the room as though she were sizing them up.

"You okay?" John asked with surprising gentleness.

She looked down as though she were concentrating for a second then lifted her chin to meet his gaze with a strange intensity. "Doctor Weir is fine," she intoned.

Sheppard shifted his weight and his whole posture changed. "Doctor Weir doesn't talk about herself in the third person," he said tightly.

"She was simply overcome by the effects of the imprinting," she replied with a clinical detachment that was not like Weir at all.

Caldwell reached up and touched his comm. "Security team to the infirmary."

"That's not necessary Colonel..." She dragged off thoughtfully. "Caldwell," it was like she plucked the information from inside Elizabeth's brain. "She is simply harboring my consciousness," not Weir explained.

"Here we go again!" McKay exclaimed throwing his hands up in the air.

"And you are...?" John dragged off tightly. He didn't like this, not one bit. If she could access the information in Weir's mind there was no telling what this stranger could do.

Not Weir turned to face Sheppard. "I am Phebus," she said her tone still flat. "We are a race of explorers. On our journey home our vessel was attacked."

"By the Wraith?" Caldwell asked suspiciously.

"Yes," she responded quickly. "We were forced to abandon our ship and launch our escape pods. If this has happened to me than I have been adrift for some time and the pod has determined my body is beyond resuscitation."

Beckett pressed his lips together sympathetically as he stepped up next to the gurney. "You're quite correct I'm afraid."

Phebus turned to face Beckett. "Than for all intents and purposes I am already dead."

"I'm sorry," Beckett said.

"So am I," Phebus agreed.

"Yeah, yeah, yeah," John grumbled. "We're all very sorry. Where's Elizabeth?" he snapped impatiently. 

Phebus smiled at him gently. "She is here also," she assured him reaching up and lightly touching the tips of Weir's fingers to her temple. It was odd to watch her move Weir's body. She didn't move like Weir did and she seemed just as uncertain of how it moved and responded. 

"And I supposed you'd like us to take your word for that?" Caldwell asked sharply.

Phebus raised her eyebrows at his tone but didn't look offended. "Would you like to speak with her?" She asked simply as though they were all children who hadn't considered asking the right questions.

"Yes we would," John agreed.

Phebus bowed her head respectfully and closed her eyes, hanging her head. Weir's body shuddered and she gasped, her eyes snapping open as she collapsed back against the pillows. She raised a hand to her forehead and grimaced looking like Elizabeth once more.

"Doctor Weir?" Caldwell asked in concern.

Beckett moved to Weir's side, catching her arm and steadying her. Elizabeth laid a hand over the top of his, giving it a small squeeze. "It's okay Carson," she promised him in a gentle tone, then she turned to the others. "I'm fine," she assured them.

"Elizabeth," John said cautiously, his eyes flickering over where Elizabeth was still covering Beckett's hand with her own. "I'm not sure if you're aware of this, but there's another um..."

"I know," Elizabeth quickly assured them. "Her name is Phebus."

"You seem remarkably sanguine about all of this," McKay said with a scowl. He had been significantly less so when he had a second consciousness in his mind.

Kai was watching Beckett however who was staring at Elizabeth in confusion. Her eyes drifted over where their hands were still touching. Beckett seemed as confused as the rest of them. Elizabeth met Kai's eyes and followed her gaze to where her hand was. She quickly pulled it back as though she had just realized she was still touching Carson. It seemed off. Kai frowned, she tried stretching her psychic senses out but the only thing she could feel was Sheppard.

A frowned formed on his face and she pulled back, not wanting to push it if it was going to effect him. She didn't know enough about her abilities to even know if it was something she could feel. She wished Teyla were here, she was better with her own psychic abilities, although hers were based on her wraith blood so there was no telling if they would be any more helpful than Kai's.

"Well, the imprinting," she stumbled over the word. "Will only last a matter of hours." Elizabeth paused for a moment to catch her breath then her eyes widened a little. "The other pod!" she exclaimed. "Phebus urgently desires to be here when we bring the other pod back to Atlantis."

Sheppard shot Kai a fast look, so she wouldn't say anything about the pod. She dipped her chin in understanding and kept her face devoid of emotion. Sheppard crossed his arms over his chest. "Why?" he challenged, not interested in giving this other consciousness anything it wanted until they could be sure of it's intentions.

A small private smile tugged at Elizabeth's mouth. "She believes it's her husband," she said as though it were a little ridiculous, but she wasn't going to argue with the other consciousness in her mind.

"Husband?" Caldwell clarified.

"Yes," Elizabeth agreed in a rush. "She believes he escaped the ship, in fact she's certain of it..." she shivered and blinked in surprise.

"Elizabeth?" Beckett asked gently, his face a mask of concern as he stepped close to the gurney again.

"Ah, the rush of emotion it's ah...overwhelming," she said lifting her shoulders and smiling as though she were experiencing the feelings of love and excitement herself.

"I can imagine," John said uncomfortably, shifting his weight. He didn't like this, not one bit. He knew when Elizabeth decided something like this there was no talking her out of it.

McKay shot him a look. "No, no, you can't."

John pulled back. "No," he agreed. "I can't."

"John, I'd like you to try," Elizabeth said and Kai stiffened looking back and forth between them as she immediately realized what Elizabeth was about to ask.

John wasn't following, he looked back and forth from Elizabeth to Kai who suddenly looked even more pissed off than she had been before.

Elizabeth smiled. "Phebus has a favor she'd like to ask of you," she said with a grin.

John pulled back with a frown but he didn't immediately say no.

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Sheppard, Caldwell, McKay and Kai were all back down in the east pier lab standing over the second life pod. Kai was running over the data from the first imprinting over and over again, trying to discern if there was some way to achieve access to the consciousness without Sheppard taking it in himself. She hated that he had agreed, but she couldn't exactly argue with him about it in front of everyone without seeming heartless.

McKay was standing at the terminal, looking at Sheppard and Caldwell as he explained all they had learned. "As I understand it the beam that hit Elizabeth was part of a fail safe feature built into the pod system. As cellular deterioration progressed the pod stored her consciousness in a sort of ah flash memory."

Caldwell frowned. "But why? I mean what good is the technology if the effects are temporary?"

"Black box," Sheppard said suddenly.

"I mean that makes sense," McKay agreed. He turned to Kai. "It's why you couldn't find any information about the pod or what happened. This way even if the occupant doesn't survivor they can still report what happened to their ship in person. Rescue teams could interrogate them even if they were incapable of regaining consciousness."

Caldwell shifted his weight and frowned. "You're talking about a human flight recorder. That's pretty dark."

"A useful thing in times of war," Sheppard said grimly as he stared down at the pod. He wasn't crazy about taking on this other consciousness, but he also wasn't going to volunteer anyone else to do it. Weir felt strongly about it and he wouldn't argue with her over a humanitarian mission like this. So far there had been no military reason not to go through with her plan. It was rare they had missions with happy endings, and if they could give these two explorers one after what the wraith had done to their people he wasn't about to argue about it.

Kai nodded. "It would be more accurate than anything the computer could come up with. And if the people are trained to expect such a thing, it would hardly be jarring."

"It could also be the means for two survivors to say one last goodbye," McKay said with feigned compassion.

Kai shot Sheppard another disgruntled look. She didn't like this idea one bit. She opened her mouth to say something but bit back her words when the door slid open behind them. Beckett pushed Weir in ahead of him in a wheel chair.

"Are you sure she's up to this?" Caldwell asked Beckett grimly. The Colonel had not been so silent about his feelings that this was a bad idea. It was a uselessly reckless act that would unnecessarily take out both the leaders of Atlantis. Although he did respect Sheppard's decision not to allow any of the people under his command to take on the risk themselves.

"Physically she's perfectly fine," Beckett said brightly. "Besides Elizabeth wouldn't take no for an answer."

Elizabeth smiled indulgently. "Well, love is a powerful thing Carson," she said reaching up and touching his hand where is rested on the wheel chair over her shoulder. The movement didn't go unnoticed by Kai once again and she found herself wondering if there was something more than just friendship going on between the leader of Atlantis and their Doctor.

Sheppard scowled. "You're a hopeless romantic, you know that?" he grumbled.

Elizabeth smirked up at him. "Well, you're just as hopeless. Otherwise you wouldn't have agreed," she countered.

Sheppard pressed his lips into a line. He didn't really have anything he could say. Elizabeth cut her eyes to Kai's back and smirked at him. John shifted uncomfortably not liking the direction the conversation had taken.

"I've gone over the respective EEG patterns and I can say with some degree of confidence that this imprinting that Doctor Weir's temporary occupant calls it won't last more than a few hours," Beckett said standing beside Elizabeth.

"You can guarantee that?" Caldwell asked sharply.

"A day at most," Carson assured him soothingly, cutting his eyes over to Weir.

"Well, I'm sold!" McKay said brightly. "Shall we?" he began typing on his tablet. "And..." he dragged off as the pod door slid open to reveal a male in a different style flight suit.

Kai frowned looking back and forth between the two bodies. The flight suits were both different, not just color but also styles.

Beckett checked his readings. "Still alive," he confirmed. "Just as before, life signs even fainter than the first one. If we're going to do this, we have to do it now."

Caldwell turned to Sheppard. "I'd prefer if this alien consciousness weren't armed."

"Right," Sheppard agreed. He pulled his gun and held it out to Kai without thinking about it. She took it and tucked it into the back of her pants than held her hand out for his knife. He looked down at her with a frown.

"Someone in your body could do a lot of damage with a knife," she said emotionless as she raked her eyes up and down his body.

Sheppard bit back a smirk as Kai ran her eyes over him, he grunted and pulled his K-BAR handing it to her. She slid that into her belt as well and stepped back to her station.

"Colonel Sheppard," Beckett said. "You'll have to be in close proximity to the pod for the transfer to happen."

"Yeah, yeah, I got it."

"But you're not moving," Beckett pointed out gently.

Sheppard shifted his weight and his eyes flickered from Kai to Elizabeth. "You know they were husband and wife. Anything could happen."

Elizabeth's head hung and her body shuddered. She drew in a sharp breath and when she raised her head it was clear by her posture that Phebus was back in control. "I promise to be discrete Colonel," she said dryly.

"Well...I guess, I'll see you guys later," Sheppard stammered.

"Have fun," McKay said sarcastically stepping aside so Sheppard could approach the life pod.

Sheppard stepped up next to the pod and the beam of light hit him in the face. He didn't fall however, instead his whole body tensed and he caught himself on the edge of the pod.

Kai felt a wave of pain through their connection that actually made her stagger. She knocked a container off the station she was standing at and Beckett's eyes flew to her for a second. She opened her eyes and stared at John in alarm. Elizabeth never mentioned pain that came with the imprint. For her to feel it through the connection meant it was an incredible amount.

"Give him a moment," Phebus said soothingly as though it were nothing.

John hung his head as his body shuddered and Kai wondered if it was hurting him more because he was fighting it. He stilled and the pain disappeared but so did their connection. In a rush Kai was all of a sudden very alone in her head. She sucked in a surprised breath as Not-John lifted his head and quickly took in the room around him.

"Thalen," Phebus said his name cautiously as she watched him. "It's me," she said and a slow smirk stretched Elizabeth's face.

He looked around once more before he frowned in confusion at her. "Phebus?" he asked, still sounding disoriented.

Kai cupped her forehead. She felt almost nauseated and couldn't quite seem to focus. Beckett was the only one who would have noticed, however everyone's eyes were locked on Sheppard and Weir.

"It's all right these people recovered our pods. We may well be the last of our kind," Phebus stepped around the pod towards Thalen. He tensed, shifting his weight so he was facing her straight on. He flexed his hands as though testing them out. "These generous people have allowed us to be together one last time."

Thalen turned to the room. "You consented to this?" he asked in disgust.

Phebus quickly took a step forward. "One last chance to say goodbye to my husband," she said. Thalen frowned but she crossed the room in two rapid strides and grabbed him by the back of the neck, pulling his lips down and mashing hers against his.

Kai's eyes widened and the whole room fell away as she watched Elizabeth kiss John. Even knowing it wasn't John, she felt a deep swell of possessiveness rising in her belly. Phebus deepened the kiss and he didn't resist. They were both a little breathless when they broke apart. 

"That's not what I expected," he said, still looking a little confused.

"I know this body is different," she said looking down at herself self-consciously. "But I assure you Thalen it's me."

He nodded slowly, a calculating look in John's hazel eyes.

"Is it possible for us to be alone, just for a few minutes?" Phebus asked, but she never took her eyes off of Thalen's.

"No, absolutely not," Caldwell said quickly.

"Oh," Beckett tsked. "Don't be so heartless," he admonished, watching the two of them with a warm smile.

"They are both consenting adults," McKay pointed out.

"No," Kai snapped, her jaw tight. She was starting to feel more like herself again, but she was still breathless.

"That's not what I'm concerned about Doctor," Caldwell told McKay.

"The Colonel's right," Thalen agreed.

"Doctor Weir is in charge of this facility," Phebus said in that strange emotionless tone of hers.

"I'm just saying there should be an armed guard outside the door," Thalen filled in.

"Two guards, one at each door," she corrected raising her eyebrows.

Kai tensed as she looked back and forth between the two of them. Something was happening. Something they were missing. It was impossible to know however when neither Weir nor Sheppard were in control of their own bodies.

"I've already taken that precaution," Caldwell snapped. He was getting more and more tense as this went on. He was maybe the only other person in the room even close to being as uncomfortable with the whole situation as Kai.

"Of course they are," Phebus agreed. In the same moment the two of them whirled away from each other and bolted for their doors.

Thalen punched the guard and took his stunner. Firing shots into the room. He turned, looked Kai straight in the eye. "Kai," he said her name emotionlessly as though reading it off of a list. He cocked his head to the side, running his eyes over her in a cold, clinical way. "Really?" he asked with a shake of his head, he lifted the stunner and pulled the trigger. The stunner shot hit her in the center of the chest and she went down, hard.

"Security to lab three!" Caldwell yelled into his radio and Thalen stunned him next. McKay crawled over to Kai's unconscious body and pulled Sheppard's gun from her belt. He fired blindly towards the door.

"Rodney don't shoot!" Beckett yelled. "That's Colonel Sheppard!"

The shots however scared Thalen off and he ran.

"I'm sorry I-" McKay started to say standing up.

Phebus stalked back in the room and pointed the other stunner at his chest. He raised his hands in the air.

"You two need some very serious marriage counseling," McKay said breathing heavily.

Phebus scowled at him. "He's not my husband you idiot, he's the enemy. Drop your weapon," she ordered.

McKay immediately threw the gun away from him.

"Now radio security and tell them everything is fine."

Beckett charged her, unable to believe he had been fool. "Everything is not fine-" he started and she stunned him in the chest emotionlessly. "Rodney," she said teasingly.

McKay reached up and touched his ear. "Security this is Rodney McKay. Everything is fine, never been better, Colonel Caldwell was kidding when he said what he said he-"

Phebus sighed. "Oh forget it," she grumbled and she fired a shot straight at McKay's chest. She looked over the unconscious group and disappeared out the door, gun in hand.

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Hope you enjoyed the update! We reached 20k reads today and I am so excited. Thank you all for your incredible support. When I first began writing this I never imagined so many people were still out there who love SG-A. It is your support; votes, reads and comments that have kept this story going! Thank you all!!