Author's Note: This tag to "The Long Goodbye" begins immediately after the episode ends. It is the first story co-authored by Merlin71 and Titan5, but hopefully not the last because I, for one, have had a blast. Personal thanks to Shelly (Merlin71) for having the great idea to do this!

Disclaimer: Unfortunately we don't own the characters or the show and our only payment is the warm fuzzies we get from writing and from reading reviews.

What's Left Behind – Chapter 1

As Caldwell left, Elizabeth shrunk down farther into the bed, making herself as small as possible. She made a point of not looking at John, certain that her face was probably red after Caldwell's mention of their kiss. She had a sinking feeling that it would be a while before they lived that little moment down.

Thalan picked up the PDL and began making a show of working on it again, trying to figure out a new plan. He'd faked the convulsions in order to convince them that he was gone and John Sheppard had returned. It had pretty much worked, but there was still one major hitch. He was stuck in the infirmary with no way to escape without tipping his hand. He wasn't sure how long he had left, not long in all probability, but he didn't want to spend it locked up. Phoebus was gone, so he guessed that meant he'd won. Little good that would do him. Some time in the next few minutes or, if he was lucky, the next few hours, he would cease to exist. Talk about a hollow victory.

He allowed himself a sideways glance at Elizabeth. She was a very nice and beautiful woman and he was suddenly glad he hadn't had to kill her just to get to Phoebus. Sheppard was glad, too. He laid his head back against the pillow, rubbing his hand against his forehead. The headache he'd been fighting all morning was really starting to throb and he noticed his arm was beginning to ache as well.


He put his hand down and looked over at Elizabeth. "Yeah?"

"You okay?"

Thalan smiled at her. "I'm okay. Just a bit of a headache. Can you blame me? It's not every day the expedition leader chases me all over Atlantis, trying to kill me."

Elizabeth sighed. "I'm really sorry about that. I promise that wasn't me."

"I know, it's okay. It wasn't me either and I did some things I'm not very proud of. Rodney says it'll be a while before they get the power repaired completely."

"You should probably tell Carson about the headache, though. He'll want to know."

Thalan sighed, wishing he hadn't said anything. "I will," he lied. He laid his head back against the pillow again. "I think I'll just close my eyes for a few minutes."

He awoke to find a nurse fussing over him, surprised that he had fallen asleep, and even more shocked that he was still alive. His headache was worse and he groaned softly, bringing one hand up to rub his temples.

"Colonel, I'm afraid you have a bit of fever. I'd better go inform Dr. Beckett," the nurse said.

"Great," he muttered. He glanced over to find Elizabeth watching him, concern in her face. "How long did I sleep?" He was anxious to know the time. He knew he couldn't have much time left and it wasn't looking like he would get to leave the infirmary.

"Not long, about an hour. You were mumbling in your sleep. You kept talking about Phoebus."

Thalan felt his gut clench with fear. "What did I say?"

Elizabeth shook her head. "I couldn't understand most of it. I just caught her name a couple of times."

They were interrupted by Beckett's arrival. "Colonel, Katie tells me you have a fever. I need to check the injury to your arm. I was afraid it might be a source of infection because it took so long for you to get treatment."

Thalan relaxed back into the bed as Beckett and the nurse removed the bandage from his left arm. He winced as Beckett probed the injury, sending hot pain shooting up into his shoulder.

"I'm afraid you do have an infection going, Colonel. I'll need to clean this out a bit more and get you started on some antibiotics. We'll be back in a minute and get you fixed up."

And now he was sick. He closed his eyes and willed for it to be over. He'd desperately wanted to live, to keep this body and start all over. But he knew there was no way to make it happen. He was just lying here, waiting to die, waiting for a lifetime of pain to end. He laughed. Maybe he should have just let Phoebus kill him.

"John, are you okay?"

He looked at Elizabeth once again. She seemed so concerned for Sheppard. He briefly longed to have someone care for him, to be concerned about whether he lived or died. "You have no idea how lucky you are, do you?" he asked, directing his question to Sheppard, but confusing Elizabeth.

"How lucky I am?" she asked, frowning.

He smiled. "Never mind, I was just talking to myself."

Beckett and the nurse returned and began to clean the wound again, not particularly a pleasant process. He grit his teeth against the pain, almost laughing at the possibility that these were his last moments of life. He supposed it was fitting payment for the life he had lived. When they had finished, they dressed the wound and gave him several pills to swallow, followed by Beckett tucking him back into bed.

"You need to get some rest, Colonel. One of the little pills I just gave you should take the edge off the pain and help you sleep." Beckett patted his leg. "Good to have you back."

Thalan just smiled, resisting the urge to laugh. If only they knew. He wondered if Sheppard would tell them. He lay there, thinking of the things he'd done in his life and what he'd change if he could as he drifted off to sleep, realizing that he would probably never wake up.


Elizabeth sighed as the nurse pushed the wheelchair to another section of the infirmary. "I can walk, you know. There's nothing wrong with me."

The nurse just smiled. "I know, but Dr. Beckett thought this was best, you know, just in case."

The nurse pushed her up to Ronon's bed and set the brake. "I'll be back in a few minutes to get you. Call me if you want to go back sooner."

Elizabeth nodded. "Thank you." She turned back to Ronon's bed, noting the tubes and wires running in and out from under the blanket. The steady beat of the heart monitor was a comforting and familiar sound. She'd heard it all too often when visiting members of Sheppard's team in the infirmary. But it always meant that they were still here, still with them.

"Dr. Weir?"

Elizabeth startled. She hadn't realized that Ronon was awake. "Ronon, how do you feel?"

Ronon winced as he shifted in the bed. "Been better."

Elizabeth forced herself to smile, trying to ignore the heaviness in her chest as she watched the pain flare in his eyes, the pain that she had caused. "Ronon . . . I'm so sorry. I . . . I just wish . . . I mean I tried . . . " She felt the tears well up in her eyes and her voice began to crack. What do you say to someone you shot and almost killed?

Ronon eyed her for a second before responding. "It wasn't you. I don't hold you responsible."

Elizabeth felt an odd laugh start to build inside her and she rushed to squelch it before she looked like she was totally off her rocker. She'd almost killed the man and that was all he could say. Talk about a man of few words.

"I know that, but still – I can't forget that I pulled the trigger. It wasn't me, and yet it was. I just want you to know that I'm sorry and that I would never do something like that on my own."

"I know that, Dr. Weir. Dr. Beckett says I'm going to be fine. Maybe when I'm out of here, you can show me how you took out Lorne's team by yourself."

Elizabeth smiled. "You know, I've been trying to figure that one out myself. It all happened so fast. I never would have imagined I could do something like that, even with someone else in control."

"I could show you some moves, help you defend yourself in the future."

"Just as long as I'm the one in control this time. Watching yourself harm the people you care about . . . well, let's just say I don't ever want to go through anything like that again."

"We're all still here and everyone's going to be okay. That's what's important."

Elizabeth nodded and patted Ronon's hand. "You're right. Thank you."

"Ready to get back to your bed?" asked the nurse as she walked up and released the brakes.

Elizabeth gave a strained look at Ronon. "Not really, but I don't guess I have a choice." She waved at Ronon as the nurse turned the wheelchair around. Ronon nodded as she lost sight of him and she felt much of the weight she'd been carrying lift, although she knew the guilt would always remain a part of her.

As the nurse wheeled her closer to her bed, she looked up to see Beckett and a couple of nurses working with John. He was stirring restlessly beneath the covers and kept trying to push them off, mumbling in his sleep. They had started an IV while she'd been gone and Beckett was looking concerned. She climbed into her bed, carefully watching the events taking place in the bed next to hers.

"What happened?" she asked the nurse, still standing beside her.

The nurse followed her gaze. "I'm afraid Colonel Sheppard's temperature went up rather quickly. They're trying to get it down."

Elizabeth continued to watch as the nurse took the wheelchair away. After several minutes, Carson finally came over to see her.

"Carson, what's going on with John?"

Carson sighed heavily. "His fever shot up dangerously high all of a sudden. I've started him on IV antibiotics and we're trying to keep him under a cooling blanket. I'm starting to wonder if having Thalan inside him might have somehow weakened his immune system. It's unusual for an infection to become this serious in so short a period of time. How have you been feeling?"

Elizabeth raised her eyebrows. "Me? I'm fine. Just getting a little bored is all. Is he going to be okay?"

Beckett nodded reassuringly. "I'm sure he will. We just have to give the antibiotics a chance to kick in and keep his temperature down. I'll send out for a supper tray. You need to get something to eat."

Elizabeth nodded. She wasn't really hungry now, but she wanted to keep her strength up and keep Carson happy. "When do you think I'll be released?"

Carson smiled. "Well, I think if you feel all right and your tests look good, I may release you tomorrow." He turned to look back at Sheppard. "It looks like the Colonel will be keeping us company for a few more days, though."

"Oh, he'll love that," she said sarcastically.


John could no longer tell where he ended and Thalan began. It had been so simple at first. He's spent most of the time screaming at Thalan to let him out, let him control his own body again. Sometimes Thalan seemed almost apologetic at holding John hostage in his own mind and then sometimes he seemed to enjoy the fact that he was in full control. He'd watched helplessly as Thalan let Ronon be shot, but was thankful when he at least called for a medical team.

Everything was different now. He thought he remembered something about a fever. Maybe that had something to do with the hell he was presently living in. Everything kept shifting and changing and he could barely keep up. First they were in a helicopter, artillery bursts exploding all around them. The chopper lurched violently to the left as they were hit and John glanced at the copilot's seat to see his friend no longer had a face, blood splattered on the front glass as well as on John's uniform and the side of his face. He wiped the blood away, aware that Thalan was living this part of his life with him. "We're going down!" he yelled.

He was suddenly flying a ship unfamiliar to him, and yet he was flying it as if he was born to it. He was firing the weapons at other ships, engaged in a desperate battle in the emptiness of space. The ship weaved and spun and darted as he caressed the controls. He knew he was now living part of Thalan's life. The ship rumbled and shook as they took fire.

But then they were in a jumper. He was at the controls and someone he didn't recognize was in the copilot's seat. Thalan. They were being chased and firing drones in an attempt to fight back, although he wasn't sure who they were fighting against. The jumper lurched as explosions buffeted the ship.

"What do you want?" he yelled as he tried to regain control of the jumper.

Thalan sat there calmly. "I want you. I want your life."

"Yeah, well there's a problem with that. I'm not quite ready to give it up. I'm still living it. Aren't you supposed to be gone by now?" He pulled the jumper up and around, dodging another blast of whatever was being fired at them.

"I am supposed to be gone, but I'm not. And I'm discovering that I'm not quite ready to die just yet. The last time I checked, I was in charge here, and I think I'd like to keep it that way."

Sheppard slammed the jumper to the right as another blast rocked the ship, almost throwing him from the seat. "Could we discuss this somewhere besides a war zone? Who's trying to kill us anyway?"

Thalan smiled. "Not us. You."

Suddenly John was spiraling through the darkness, losing all sense of control. This couldn't be good.


Elizabeth lay on her side, watching the nurses come and go, checking John's IV, pulse, blood pressure, and temperature. He shifted and moved restlessly, talking and mumbling until late in the night. Suddenly he bolted upright and sat in bed, staring straight ahead, his face sweaty and pale in the dim light.

"John?" Elizabeth got out of bed and went to his side, placing a hand on his arm. "John, what is it? Can you hear me?"

Slowly he turned his face towards her, his eyes glassy with the fever. "Can't . . . Thalan . . . help me." His eyes drifted closed and he slumped over against her.

She caught him and lowered him back down to the bed, her heart beating wildly in her chest. She could feel the intense heat radiating from his fevered body as it pressed against her. "John? John, can you hear me?" She stood back, brushing the damp hair from his forehead.

His eyes flashed open and he shivered. "Please," he whispered, before closing his eyes again and going limp against the mattress. She could feel his body trembling, almost like electricity was surging through it, scaring her.

"Carson?" she called, surprised at the shrillness of her voice.

Beckett appeared almost instantly. "Elizabeth, what's wrong?"

"He sat up and spoke, but now . . . Carson, should he be shaking like this?"

Beckett gently, but firmly took her arm and pulled her away from Sheppard. "I need you to get back to bed and let us have a look."

Recognizing that she needed to get out of the way, Elizabeth crawled back onto her bed as two nurses joined Beckett around John's bed. There was a sudden flash of movement and then more medical personnel appeared. Amidst all the questions and commands being thrown around at a dizzying speed, the one thing she heard clearly was when Beckett announced John was seizing. She curled up on her side and clutched her blanket, wondering how everything could have looked so good that morning, only to look so bleak now.

Elizabeth lay watching the parade of activity next to her bed for several hours. Medical personnel came and went, adding monitors and injecting things into John's IV, checking his temperature, desperately trying to get his fever down. The restless thrashing from earlier had been replaced with an eerie stillness that gave Elizabeth the shivers. Carson would make eye contact ever so often and nod, letting her know they were doing everything that they could.

When she thought she couldn't stand it any longer, Carson finally came over to her bed. "Elizabeth, how are you holding up?"

"I'm fine, just worried about John. Is his temperature starting to come down yet?"

Beckett sighed and shook his head. "Not yet. I've loaded him up with as much fever-reducing drugs as I can, but it doesn't seem to be doing any good. We're going to have to try something more aggressive. I know you can't be getting any sleep with all this commotion going on next to your bed. I thought I might move you so you can get some rest."

"No, not a chance. I'm staying right here where I can see what's going on. I won't sleep even if you do move me, so there's no point." Elizabeth stared hard at Carson, willing him to let her stay.

Carson hesitated, looked at John in the next bed, and then back at her. "All right, but stay in bed and at least try to get a little rest."

"I will. Thank you, Carson."

"We'll have to put up some privacy curtains for a while. I'm going to try giving him the equivalent of a tepid sponge bath and see if that will help cool him off."

Elizabeth nodded. "You'll let me know if works?"

"Aye, I will. Try to get some rest." Beckett moved off to the side of the infirmary and began giving the nurse some instructions. Several minutes later, they had privacy curtains set up around John's bed. She watched two nurses carry in a basin of water and some towels. She crossed her fingers, wishing with all her might that this would work.

At some point, she must have dozed off, because she woke up to find the privacy curtains down and only one nurse keeping watch over John. Dim light filtered in from the windows in the hall, letting her know it was almost daylight. She rubbed her eyes and sat up, catching the attention of the nurse checking John's vital signs.

"How is he?" she asked, the hope clear in her voice. The nurse smiled at her and she felt her heart flutter in her chest.

"Better. His temperature is finally starting to come down."

Elizabeth collapsed back against the pillows, feeling like a great weight had been lifted for the second time in less than twenty-four hours. She let her breath out slowly, the relief taking hold as the fear finally began to lessen. John was going to be okay.


John felt as though he'd done battle and lost. He was exhausted, sick, and in pain. He struggled to come to consciousness, to scream to someone that Thalan was still there, but he could never seem to quite make it. He'd almost surfaced once, had even managed to utter a few words as Thalan pulled him back under, but to no avail. He hadn't been able to make Elizabeth understand. Now he simply felt like he fought to continue existing, as though some invisible dark force was trying to suck him under and suffocate him. In his weakness, that seemed all he could do for now – to simply continue to exist. He would not give up, however long it took. He would keep fighting for the strength to challenge Thalan again one day.


Elizabeth awoke to a hand on her wrist. Her eyes snapped open to see Carson taking her pulse.

"Sorry, lass. I didn't mean to startle you." He smiled, but his eyes and the lines on his face spoke volumes about his exhaustion.

"Carson, shouldn't you be in bed? I happen to know you were up all night with John."

"Aye, I'm headed that way in a few minutes. I had to do one last check on my two favorite patients. How are you, other than being tired? I know you didn't get much sleep either."

Elizabeth looked over to John's bed. She heard the steady beep of the heart monitor and noted that no one was hovering over him at the moment. Surely that was a good sign. "Conditional response here – how's John?"

Carson let his gaze follow hers to the still form in the next bed. "He's going to be okay. His fever seems to have peaked and is slowly, but steadily coming down. I don't mind telling you he gave us quite a scare, but he's definitely taken a turn for the better."

Elizabeth smiled. "In that case, I'm okay too. Or at least I will be after a few hours of shut-eye."

"Good. I've sent for some breakfast for you and it should be here in just a few minutes. Eat and get a little sleep. I'll check on you after I've had a bit of a nap myself, and if everything looks okay, I'll release you. Not to active duty yet. I want you to rest for a few days and let me continue to keep checking on you to make sure there are no lasting effects."

Elizabeth nodded. "I can live with that."

Carson looked at her a moment as if he was about to say something, but hesitated. Finally he turned back to her. "Elizabeth, I have a question for you. Do you have any of Phoebus's memories? Did you learn things about her that you retained?"

"Actually that's two questions, but yes and yes. Why do you ask?"

Carson frowned. "Well, while the Colonel's fever was going up and he was delirious, he was doing a lot of talking."

Elizabeth nodded. "I remember. I couldn't understand most of what he was saying though."

"Well, I only made out bits and pieces, but some of it was . . . let's just say I'm pretty sure they weren't his memories. They sounded like things from Thalan's past. There were names mentioned that I've never heard of on earth, or even since we arrived here. I was a little worried that, well, that Thalan was still with us."

"It's weird, but I do remember, very vividly, many things from Phoebus's past. It's like snapshots of her life. I'm not sure if she shared those things with me on purpose, or if they just sort of . . . leaked through. I am sure of one thing. She was full of hate. Seething, uncontrollable, totally irrational hate. I think I better understand why some negotiations fail and wars persist. The hate totally blocks out all rational thought. In the end, even though she understood that Thalan probably no longer occupied John's body, she was still going to kill him, basically because Thalan had been there at one time." Elizabeth shuddered. "I was going to kill him."

"No! Elizabeth, you can't think that way. That wasn't you."

She looked down at her hands. "I know and I keep telling myself that. But I also keep seeing my hands pull the trigger and shoot Ronon. I keep hearing my voice telling Teyla to kill John. I know that my hands would have killed John if he hadn't stunned me. It's going to take a while to get past that."

Carson placed his hand on Elizabeth's. "But you will. And we will be here to help you do it." He looked over at John. "I imagine we'll have to help him fight some of those same demons. And it's the second time for him, in a manner of speaking."

Elizabeth raised her brows. "I hadn't thought of that. I guess it is kind of a strain to face the people under your command after you've beaten the crap out of them." She thought of Lorne's team and Ronon. "Guess I'll find out about that one myself."

"Major Lorne said we should make you a one woman commando unit. You know, you may actually get a little more respect out of this little incident. The next time you yell jump, I know a few people that will be asking how high."

Elizabeth grinned. "Now that I could get used to."


"You remember the part about not being on active duty yet, right?" asked Carson sternly.

Elizabeth resisted the temptation to roll her eyes, deciding it was probably not a good attitude for the expedition leader to express. Instead, she smiled sweetly and responded, "Yes, Carson, I remember. I'm supposed to rest and take it easy for the next few days."

Carson nodded. "Good. You can change while I do the paperwork thing. You're clothes are in the chair over there."

Several minutes later, Elizabeth was back in her own clothes and waiting for Carson when she wandered over to John's bed. She placed her hand on his arm and was a little surprised to feel the hot touch of his skin. His temperature was still quite high and she frowned, wondering what had caused him to get so sick. She was staring at his face, lost in her thoughts, when his eyes fluttered open.


He looked blankly at her for a second, making her wonder if he was really seeing her.

"Phoebus?" he whispered, his voice so soft she barely heard it.

She leaned over so her face would be closer to his. "No, it's Elizabeth. Phoebus is gone."

"Phoebus . . . gone?"

She smiled and squeezed his hand. "Yes, Phoebus is gone for good. You're safe now."

He blinked a few times and then seemed a little afraid. "I'm John."

"I know. It's okay. You've had a high fever, but you're going to be okay now. You just need to rest and get better."

Thalan looked at her quietly for a few seconds, studying her face. "Tired."

She nodded, a little disturbed at his disorientation, and placed her hand against his fevered face. "Close your eyes and sleep. You'll feel better when you wake up."

He watched her for a few more seconds before allowing his eyes to close. She stayed there beside him for several more minutes, watching his even breathing and convincing herself that he would really be all right.


Thalan knew he was sick and weak. He wasn't completely sure why he was still here, but he wasn't going to argue the point with anyone. He wondered if the sickness and the fever had anything to do with his continued survival. He didn't know and he didn't care. He had somehow survived and he would continue to survive. He was finding it a constant struggle to hold Sheppard back and keep him from taking over. Although the illness had weakened him, it had weakened Sheppard even more, allowing Thalan to resume and maintain control.

He would have to convince everyone that he really was Sheppard, at least until he tired of Sheppard's life. Although others in Atlantis might be skeptical, he knew Elizabeth trusted him implicitly, especially after their mutual possession. She knew Phoebus was gone and so she assumed Thalan was as well. Having the loyalty of the expedition leader would definitely be to his advantage. He might enjoy being John Sheppard for a while. He could do all sorts of things, including some things the real Sheppard probably would not.


Elizabeth stepped into the doorway of Carson's office to see what was keeping him, only to hear Major Lorne's concerned voice.

"But how do you know she's Dr. Weir and not Phoebus? What if we're turning that maniac loose on the city again?"

Carson huffed. "Major Lorne, I assure you that Phoebus is gone and Dr. Weir is back. You'll have to take my word for that."

Elizabeth smiled and crossed her arms. "I'll try not to act like a maniac any more, Major Lorne."

Lorne spun around as his face turned bright red. "Ma'am . . . I'm sorry, I'm just concerned for the city. I didn't mean anything against you."

Elizabeth arched one eyebrow and sighed. "Are you sure you're not just worried about getting taken down by a girl again?"

Lorne was speechless. He just stood there, opening and closing his mouth several times before finally giving up.

Elizabeth waved her hand at him. "I'm just kidding, Major. I understand your concerns, and I would reassure you that I am me if I thought it would do any good. I guess you'll just have to keep your eye on me for a few days."

Lorne still looked uncomfortable. "Yes, ma'am." He quickly exited the office, looking at the floor as he squeezed past Elizabeth to get through the door.

"I think you scared him," said Carson, his eyes twinkling.


THE END . . . of part 1.