Disclaimer: I do not own Stargate: Atlantis. This is fanfiction.

A/N: Just an old file I found. It was going to be a multi-chaptered story but it kind of fell to the wayside. If there is enough interest, I may come back to it but for now, it will remain as a one-shot. And despite its ambiguous plot, I do hope you enjoy it.

The first thing Elizabeth noticed was the pain in her skull. She felt like she had been on a roller coaster more times than she can count and now her head and stomach was paying for it. Groaning, she lifted a hand to her forehead, wincing as she tried to rub the discomfort away.

She vaguely remembered being off-world with an exploration team, where they had decided to do some research on an abandoned temple… but then something happened. Her memory was foggy but she suspected it was the doing of some sort of relic. She frowned and listened in for her team but all she heard was dense silence.

She snapped open her eyes, only to shut them when the blinding light pierced her eye sockets. She recognized the familiar lighting as the ceiling around most of Atlantis. However, why she was back on base she had no clue.

Letting her eyes adjust slowly, she pulled herself up to a sitting position and clenched her jaw as the world spun around. She must have hit her head hard when she fell. She could feel the pulsing ache on the back of her skull. Looking around, she suddenly realized that she was sitting on the hard floor, rather than the soft beds of the infirmary.

"Carson?" she called out hesitantly. She was awkwardly surprised when her voice cracked and her words were rasped out. She tried to swallow through her parched throat as she quickly assessed her situation.

It appeared she was in an empty room with no windows and only two cots on opposite sides. Shivering, she realized that there was no heating either. She had immediately assumed she was back in Atlantis because of the interior design but what reason would her people have to put her in here?

Trying not to panic, she got to her feet slowly, feeling the soreness that came from both the incident and lying on the hard floor. Testing her feet, she stumbled over to the door to open it. She wasn't at all surprised when it didn't. What she needed to do now was to figure a way out of here.

Spotting a cot in the corner, she went over to lay down, her body taking in the comfort despite the scratchy fabric. She had only wanted to lie down for a while but she must have been more worn out than she had thought. Within minutes, she had fallen to sleep.

The next time she opened her eyes, she panicked. The room was darker this time around but it was the presence of another that had her hairs standing on end. Quickly, she sat up and stared at what she assumed to be his face in the dark.

"Who's there?" she demanded, glad that her voice came out clear and strong.

He didn't say anything, choosing to take a few steps into the light. When she saw the familiar face, she gasped. "John!"

The man winced at the name but Elizabeth took no notice. "They got to you too? Oh, god, are you alright?"

She rushed forward to check him out but faltered when he immediately backed away.

"What's wrong?" she asked as she reached a hand out to his arm. What happened next was something she didn't expect at all.

"Don't touch me!" he snapped, smacking her hand away. He looked at her with a face of disgust.

Feeling hurt and somewhat confused, Elizabeth backed away as well. "What's wrong with you? Did they do something to you?"

"What's wrong me?" he repeated incredulously, sounding more gruff than Elizabeth was used to. "What's wrong with you? Looking at me like I'm your friend… it's your fault we're in here!"

"My fault? I don't even remember what happened," she retorted, feeling a bit defensive. If tampering with whatever she could have tampered with was what got them here, then she knew the blame would be on her but John had never attacked her like that before. It was unnerving.

"Whatever," John muttered, looking at her like she was crazy. He started pacing on his side of the room, keeping clear away from the brunette.

"What happened to your hair?" she suddenly asked, taking note of his crew-cut. It was the one thing she could have never imagined John without—that signature bed-head that had girls swooning when he walked by—and here he was, stalking furiously across the floor with a close shaved head.

"Nothing happened," he responded coldly.

Okay, he was still angry, she thought to herself. Settling on the cot, she absentmindedly rubbed the bruise on the back of her head as she thought over their predicament. Whatever happened in the temple led to their imprisonment. By who, she had no idea, and from the look of things, her captors haven't been to see her for several hours. John on the other hand, may have been interrogated already, considering his attire and mood. She didn't know the status on the rest of her exploration team however.

"Do you know if the others are okay?" she tentatively asked into the silence.

"How should I know?" he glared, as if she was some annoyance he didn't have time to deal with. Elizabeth frowned when he turned away from her and buried himself onto his cot.

"John?"

He didn't answer, choosing to ignore her.

"John, I'm sorry. If it was my fault, I'm sorry. I hit my head rather hard. I can't recall what happened at the temple. If I had known it would compromise our mission, I never would have done it at all."

She was met with more silence.

"Why are you acting like this?" she demanded, starting to feel angry with his attitude. "Don't you think this is too much?"

"I could ask you the same thing," he finally snapped, voice muffled against the wall. "You must really be losing it. What's with all the bullshit about a temple? Seriously, that's the best excuse you can come up with? Fuck you."

Elizabeth was taken aback. He had never cursed around her before. Something really was wrong with him.

"You're not him, are you?"

He shifted around on his cot to face her, frustrated that she was still speaking to him. "Not who?"

"You're not John," she repeated, as if that explained everything.

"I'm not John? Shit, you must've hit your head harder than I thought."

"You're a replicator," she said softly, feeling tightness in her chest. She wasn't sure if she could stand the idea of losing her second-in-command.

"Replicator?" he asked in disbelief, sitting straight up. "Replicators are practically non-existent! I really don't have time for jokes, Weir."

"I don't joke, Sheppard," she snapped back with equal force. Replicator or not, she knew the man before her was not the John she knew.

"Right, I forgot," he laughed cruelly. "Everything has to be your—"

At that moment, the door chose to slide open, revealing a group of gray-clad men, led by a singular man in white. Immediately, John stood up to confront them.

"Let me go or else," he growled. "My team will show no mercy when they find me. It's better to just get me out of your hair now."

"Not now, Sheppard," the leader of the group sang nonchalantly as one of his guards shoved him back to his cot. Elizabeth felt her heart stop when man in white locked eyes with her.

"Dr. Weir, how nice it is to see you again," he drawled, a sadistic grin creeping over his face.

"Have we met before?" she asked hesitantly. When it came to faces and names, Elizabeth was sure she would remember. She had exceptional memory; incredibly useful when it came to her line of work and Atlantis research.

"Don't pretend, Dr. Weir. It doesn't suit you at all," he reprimanded, smirk dropping and voice growing hard.

Elizabeth swallowed, chancing a glance at John, who laid with his back to the scene. She mentally hit herself, aware that she had subconsciously sought his protection.

"Where are the artifacts?" he commanded, dark eyes fierce.

"What artifacts?" Elizabeth was utterly confused. They had found them in the temple, didn't they? Her team couldn't have taken anything…

"The Tablets, Dr. Weir."

"The what?" she replied, furrowing her brows. "It's the first time I've ever heard of them!"

She was met with a slap to the face however.

"Don't lie. It was you who broke into the catacombs and took them. Where are they?" he snarled, slamming her against the wall.

"I don't know what you're talking about!"

"That's not what I want to hear! If you don't tell me, you'll regret it!"

"I honestly do not know!"

"Wrong answer, Dr. Weir," he yelled angrily. All of a sudden, she heard something crack and a flash of pain shot through her finger and registered into her brain. She had to bite her lip from crying out.

"If you don't tell me, I'll break the next finger. Then it'll be the next and the next, until you're out. Then it will be your arms, your ribs, your—it'll be best if you just say it now."

Tasting the blood in her mouth, she rasped out another denial, trying to plead with him with her eyes. He proceeded to snap her next appendage and added a sharp kick to her side for good measure. This time she let out a soft cry.

"Where are they, Dr. Weir? I need them!"

Elizabeth shook her head, knowing she was trapped in this situation. Even if she had wanted to tell them anything, she didn't know what the hell they were on about in the first place.

Feeling another finger break, she gasped when he also wrapped his hand around her neck, effectively cutting off part of her air supply.

"Dr. Weir, you are angering me. I do not have time for this."

Breathing heavily, Elizabeth closed her eyes, feeling the world beginning to spin around her. "I'm sorry but I don't know."

"My Lord, you are needed in the control room," a voice spoke up from the door, halting her interrogator's next action.

The man in white whirled around. "I'll be there momentarily."

He then turned to Elizabeth. "Looks like it's your lucky break. I'll be back later so you'd better cough up an appropriate answer." With that, he released her and marched out of the room with his guards.

Gasping, she winced as she struggled to move her fingers back into place. Glancing at John once again, her heart clenched painfully as she noticed that he had not moved at all from his position. Fighting the will to cry, Elizabeth curled around herself on the floor, shuddering at what was to come. She did not belong here at all. Not locked up. Not beaten for information she didn't have. And certainly not with an imposter posing as her best friend. She had never felt so hopeless before.

The next time she opened her eyes, she was on her cot, covered by a thin blanket. She briefly wondered if she had fallen asleep and to the nature of which she had the strength to reach her bed. She cast a glance at John's unmoving form on the other side of the room but shook her head at the thought. No, this John didn't care about her well-being.

Snuggling into the blanket, Elizabeth let a few tears loose. She wish she would wake up from this nightmare, which in all likelihood, probably was. She could be stuck in another replicator's hold for all she knew. However, a small part of her couldn't help but feel this was different. She didn't feel as if the world didn't belong—she felt like it was her who didn't belong.

Taking her uninjured hand, she swiped away her remaining tears, wondering what exactly could have happened in that dreaded temple.

All of a sudden, she heard some scraping at the door. Sitting up in panic, she realized that John had immediately jumped up and rushed to the only exit.

"What's going on?" she asked aloud, not expecting to receive an answer.

"Mind your own business," he hushed, crouching to the side and waiting.

"Kind of hard to, don't you think?" she muttered under her breath. They were bunked up in the same room after all.

A few seconds later, the door slid opened to reveal Ronon and Teyla. Elizabeth was momentarily relieved to see familiar faces but that hope was crushed when she realized that they too, were different from the people she once knew. Teyla had longer hair and Ronon was sporting another old scar on his arm, both of which were impossible to acquire within a few days time. Maybe she really was losing her mind.

"John, are you alright?" inquired the woman as she handed him a vest and P-90.

"Just peachy, Teyla. What took you guys so long?" he laughed offhandedly as he strapped on the vest and checked his weapon.

"Well, if you hadn't—," Ronon started but paused when he spotted Elizabeth across the room. "Dr. Weir."

"What?" Teyla exclaimed in surprise. She looked as if she hadn't seen her in years. "Oh, my."

Ronon raised an eyebrow at John, silently questioning him. His commander avoided his gaze however. "Found her unconscious outside a cave before the Elites captured us."

"You what?" Elizabeth couldn't help but ask. This added a whole new perspective to things. "What cave? The Elites?"

"Apparently, she thinks it's funny to question everything I say in a disbelieving manner," he explained further. "Teyla, you have some of that medicine we dosed Rodney with last week?"

"Yes, but why do you need it?" The warrior tilted her head curiously but reached into her vest anyway. "Here."

John quickly tore off a section of his sleeve before pouring the liquid over it. "Can't leave her here, can we?"

Before Elizabeth could register what was going on, John had grabbed her head and had the cloth over her face. Struggling furiously, she realized it must have been a chemical similar to chloroform as she was quickly losing consciousness. Feeling her mind fog up and her muscles weakening, she thought she saw concern in his eyes before darkness overtook her.

This had really got to stop, Elizabeth thought with a groaned. She had been falling asleep and knocked out so many times, it was making it hard to tell how much time had passed since the expedition to the temple.

Opening her eyes, she noted that she was in a different room from last time, this one more brightly lit and the walls a neutral color. She went to sit up but discovered that she was strapped down to a bed not unlike the ones in the infirmary back on Atlantis.

"Great, I've traded one prison for another," the brunette muttered angrily as she tugged at the restraints.

"I wouldn't do that if I were you," piped a voice from the door. The Scot strode over with a clipboard in hand, looking very much the same as the one she knew. He couldn't be the old Carson though or else she wouldn't be strapped down like a mental patient.

"Let me go," she demanded, treating him more harshly than she would've liked. It was clear that the people she once knew were not her friends anymore.

"Relax, Elizabeth. I had to put a cast on your hand. You also had quite of number of bruises across your torso, not to mention that nasty bump on the back of your head," the doctor chided, shaking his head disapprovingly.

"I don't understand what is happening!" she yelled, wanting answers. "Why are all of you acting like this? What are the Tablets?"

"We were hoping you could tell us that, Weir," spoke John from the doorway. "After all, you were the one who started all of this."

"I did not," she corrected staunchly.

"Don't lie," he growled. "We saw you take them. We also saw you escape with half the information in our database."

"Impossible!" she snapped, eyes flashing dangerously. "The John Sheppard I know wouldn't even let me go off-world without his team! God forbid I trip over a tree root and scrape myself..." She said the last bit a tad spitefully. "And why would I need to steal information from you? Isn't that defeating the purpose of being the expedition leader?"

"Expedition what?" John asked incredulously. "First you're babbling about temple nonsense, and now you're talking like you're still the leader of some expedition? Enough is enough, Weir! Or have your really lost your mind?"

"Maybe I have because I clearly can't explain what has happened since waking up in that prison," she bit back, tugging some more at her restraints.

"Tell us more about the temple, lass," cut in Carson, seeing that John was about to argue pointlessly back about her state of mind.

"How do I know you're not replicators looking for information?" Elizabeth said quietly. "Something like this has happened before. I woke up to find that I was living in a different world, a reality that wasn't mine. You're all not real!"

"Just tell us, Weir. Some insight into that sadistic mind of yours would really help," said John, shaking his head pitifully.

Elizabeth had never wanted to cuss so badly in front of her would be coworkers.

"Are you going to keep me locked up here for the rest of my life?" Elizabeth snapped when Other John finally walked into her cell. She had been trapped in the cell since her dismissal from the infirmary and was beginning to grow quite restless.

"Glad to see that your people skills are working for you," he glared. Out of all the familiar faces, she seemed to hold the most against him and it really bothered him. "Was your John such a saint?"

Ignoring the double meaning behind the implication that the real John was hers, she stalked up to him furiously. "No," she drawled. "But he was a good person nevertheless."

"Then what's your problem?"

"Besides the fact that I am a prisoner?" she pointed out, raising a brow. "And that this isn't my reality?"

"Yeah, why do you hate me?" he implored, mouth set in a grim line.

"I don't."

"What?"

"I don't hate you," Elizabeth repeated, holding his gaze. "In essence, you're John, aren't you? Isn't that how it works? I just don't like the way you're treating me—the way that you're unwilling to help me."

"Was I that horrible that you had the need to dream up a different version of me?" he growled, not wanting to play her game anymore.

"You still don't believe me?!" she said exasperatedly. "I'm not the Elizabeth you knew because—because I'm not her!"

"Forget it, I'm out of here."

"Wait!" she called. "I don't know what she's done to you but maybe it's time to let go."

He turned around to tell her to cut the crap but she holds up a hand to stop him.

"I don't know what kind of relationship you two had, or even who was at fault, but it has been two years since you've seen her. You say you're over her but clearly you're still hurting!"

"And whose fault would that be?" he retorted angrily, rounding back on her.

"You really cared about her that much?" she asked, not backing away from his form.

"I loved you," he confessed quietly. "I gave you everything and you threw it all back in my face. You're the reason why I am the way I am now!"

"You don't mean that," she said tightly, trying to ignore the fact that he just confessed past love for her. "John doesn't have close romantic relationships with women."

"Stop talking about me as if I'm someone else."

"Stop referring to me as the Other Elizabeth."

"Your John sounds like a pathetic wuss."

"That was really uncalled for."

They glared at each other for what seemed like forever. It wasn't until someone rapped on the door that they realized how close they were. John backed away nonplussed but Elizabeth stood there feeling more rattled than she felt should have.

"Enjoy your meal," he muttered before swiftly leaving the room. The woman who had knocked looked on nervously before setting the tray on the makeshift table. She nodded in acknowledgement before shutting the door.

Elizabeth sighed in frustration, sliding her back down the wall.

All she wanted was to get back home.