Author's Note: Well, here it is, lol. It didn't turn out the way I wanted it to, but then again nothing ever does -grins-. I apologise now for any mistakes, I didn't have the time to read it through. Enjoy!

Different Paths P1

By Steph7085

For once, nothing eventful had happened in, or outside of Atlantis. Normally it would be welcomed as the respite it was, but for John Sheppard it was hell. After all, he thrived on action and the lack of things to do was making him more than a little restless, which was why he found himself sitting in McKay's lab - willingly. He had to do something to alleviate his boredom, and annoying the hell out of McKay was always so much fun, not to mention easy.

The scientist in question was sitting opposite John looking incredibly harassed as he battled with his 'latest discovery', tapping the metallic looking…thing on the table top as John watched with his arms folded across his chest. He would have put his feet up on the desk, but Rodney had taken to shoving them off so he'd settled for leaning back in his chair, alternating between gazing at the ceiling and the private war between man and…machine thing.

"What the hell is that thing anyway?" John asked, righting his chair and leaning over the table to get a closer look. Rodney levelled him a glare, huffing.

"Well, I wouldn't be here trying to figure it out if I knew would I." He stated irritably. Standing up and shaking the small, rectangle device.

"Well, sorry," John drawled sarcastically, smirking as he fiddled with some random papers. "I thought you knew everything."

"I know more than you," McKay bit back. "Not that it takes much, flyboy. Don't you have somewhere else to be, instead of sitting in here annoying me?"

"Nope," John replied with a grin. Unfortunately, his response was lost on the scientist who had finally made the device do something. Rodney's eyes were focussed on a small portion of the surface which had risen, like a pillar, from the rest of it. A small white light had briefly emanated from it, before it flickered out again causing Rodney to glare darkly before shoving it on the table.

"Stupid ancients. If they were so smart why didn't they think to leave instructions?" He muttered rhetorically, marching over to a far away bench to refill his coffee cup. John took that moment to snatch the device from the table and fiddled around with it.

"I don't know, it doesn't look too hard McKay. Maybe it's just you," John teased, causing Rodney to whirl around.

"Oh, ha, ha. It doesn't seem to be working for you either, Genius."

"Well…" John began, but the device cut him off. A blinding light formed in the centre of it, and like a moth to a flame, his eyes were drawn to the light. In that instant, his surroundings disappeared as his vision darkened. Common sense kicked in and he let the device drop to the floor. It clattered noisily on the lab flooring and instantly caught the attention of everyone else in the room.

"Are you trying to give me a heart attack?" McKay cried out clutching his palm pilot to his chest. John ignored him, his focus held completely by the brunette who was so familiar, yet so, so completely different.

In an instant his emotions came crashing down like a tidal wave and he had to use all his strength to keep his face neutral. This wasn't right.

"What the hell?" He exclaimed, just as his double strolled into the room and quickly pulled his weapon out on him.


It didn't really take him long to figure out what happened. He had heard and read about stuff like this before, so it didn't take long to connect the dots. It helped that McKay had immediately jumped to the same conclusion, which had thankfully convinced himself, not to shoot himself.

John shook his head - he hated alternate realities already.

"I knew it was too quiet," he muttered to himself, shifting on the infirmary bed. His doppelganger, Elizabeth and a couple of guards accompanied him - ok, ordered him, with silent threats of violence - to the infirmary, for the obvious DNA checks and so on. He didn't mind, he would have done the same thing in this situation.

"Excuse me?" The Doctor asked, in an all to familiar voice, one that he though he'd never hear again. John looked up and smirked in his usual boyish way.

"Quiet time in Atlantis always means something bad is going to happen," he stated as if it was the most obvious thing in the world.

"Well? Is he me?" his double asked seriously, his eyes alternating between trying to see straight through John and Carson.

"Aye. It's a complete match."

"As if one of them wasn't enough," McKay cried out.

"McKay…" Alternate John growled threateningly, but John was distracted by the sound of a quiet feminine chuckle. He couldn't help but look up, his heart leaping into his throat at the familiar, and greatly missed sound. His eyes roamed over her, absorbing every detail to memory. Her brown, curly hair, a lot longer than when he had last seen her, trailed way past her shoulders and caressed the leather material of her jacket. Her face was alight with amusement, her eyes sparkling, making them look greener than usual.

As if sensing his gaze she looked towards him, her eyes briefly catching his before he looked away. He didn't need to look to know her smile had vanished to be replaced by a look of confusion and concern, so he cleared his throat and tried to rid himself of his conflicting emotions.

"Leather?" He asked, raising his eyebrows and gesturing to the jacket. Elizabeth narrowed her eyes as his double grinned.

"That's what I said."

"Oh, shut up," Elizabeth scolded playfully, slapping alternate John's arm.

"Yes, this really is fascinating. Can we get on with the explanations now?" Rodney snapped impatiently, looking towards the blonde who stood next to him and gesturing wildly. She rolled her eyes as she stepped forwards.

"As much as I hate to say this, I agree with him," she told the group as Rodney beamed smugly. "We know you've come from an alternate reality, what we need to know is how."

The group looked at him expectantly, and he couldn't help but feel uncomfortable. Sure they were his friends…and himself, but as far as he was concerned he had lost two of them, and having them here, in front of him was bringing back memories and regrets. Having Elizabeth right next to him wasn't helping matters so he jumped up and moved away. It was way too distracting.

"Well…I was in the lab, annoying McKay. I picked up that device thing, after McKay tried to beat it to death. It went all glowy, like most Ancient devices do and then I ended up in the lab, here…annoying McKay again. You know the rest."

"So you're annoying in any reality," McKay stated, before he sighed in annoyance. "Well whatever you did drained it completely. I ran some tests whilst you were getting tested."

"Well, we'll have to figure it out soon, before entropic cascade failure sets in," Sam said worriedly. "Believe me, it's not something you want to experience," she continued when she saw both John's perplexed frowns.

"We're using the ZPM to charge it up now. It should only take a couple of hours," Rodney explained. "Anyone fancy lunch?" he added as an afterthought, earning looks from everyone in the room. "What?"

"Well, you're more than welcome to look around. All we can do is wait now," Sam announced ignoring Rodney's question. "I'm sure our John won't mind escorting you around. I'll be in my office is anyone needs me." with that said she walked out of the room.

"Well Carson, can we leave now. I know I'm just dying to get out of here, so the other me must be to."

"Hell yeah," John agreed. "No offence Carson."

"Fine. You're free ta leave, but if ya feel anythin at all, anythin…" he stated warningly, giving both John's a stern glare.

"Don't worry Carson. I'll make sure he comes back if anything happens," Elizabeth soothed diplomatically, with a smile. Carson nodded and went to his office, muttering about difficult patients.

"Come on then. I don't know about you two, but I'm hungry," Alternate John said as he moved towards the doors. John slowly followed and couldn't help but notice when his other self put his hand on Elizabeth's back.


Multiple stares and whispers followed then into the mess as John's double joined the line. John didn't feel like eating and went to sit on a table in the furthest corner of the room, sinking down into his seat with a sigh.

"Are you ok?" Elizabeth asked softly, taking the seat across from him. John looked up sharply, surprised that she had followed him.

"I thought you were getting some food," he stated, more tersely than he meant to. Elizabeth looked taken aback for a moment, but she recovered quickly.

"John's getting mine," she told him softly, tilting her head to the side to try and meet his eyes. John scratched the back of his neck and tried to look anywhere but at her. Unfortunately his eyes had a mind of their own.

"Look, I'm sorry for snapping. It's just so…" he tried.

"Different?" She offered, as she rested her chin in her hand.

"Yeah," he agreed with a sigh. "You have no idea," he breathed. Elizabeth looked at him curiously, but he spoke before she could. "Why aren't you in command?" He asked absentmindedly.

She looked surprised. "Um…well, a few months ago I was injured when the Replicators attacked…"

"Rodney activated the Nanites you had in your body to save your life," he added quietly. Their gazes met for a few seconds before John looked away, suddenly finding the table interesting.

"Yes. Well, we ended up on the Replicator home world to try and take a ZPM. It went wrong and I ended up getting captured." Elizabeth told him quietly, gazing at her hands.

"We left you behind," John continued, causing Elizabeth to look up.

"No, I ordered you, him, to go," she corrected sternly, before she continued. "I was kept prisoner for a while until a rebel group of Replicators helped me escape. Oberoth had probed my mind so much that everything was so…distorted. If John hadn't come for me then I don't know what I would have done."

"He came after you?" John asked, his eyes dismayed.

"Yeah. He left Atlantis, everything, just to bring me home. Of course Ronon wouldn't let him go alone, so he had to join."

"Who had to join what?" Alternate John asked as he placed a tray in front of Elizabeth and sank down into the chair next to her, his own tray in front of him. Elizabeth quickly stole a chip from his alter-self's plate, earning a playful scowl. She just smiled back innocently, putting the chip in her mouth as she protected her own plate from his retaliation.

John felt like someone had kicked him in the gut, as the regret and self recrimination settled over him. If only he had followed his instincts instead of orders.


The last hour had passed by in a blur. John had barely listened to anything his doppelganger or Elizabeth had said, and only nodded when he though it was appropriate. It couldn't stop his thoughts from drifting to what-ifs, and the grief that he had buried and hidden threatened to overcome his weakened control. He knew that Elizabeth could tell something was wrong. Hell, she always could read his mind, and the concerned glances she kept giving him made her worry obvious. He just didn't know how to act. He couldn't bare talking to her, looking at her, and touching her, having her back, just to loose her again.

It was heaven and hell all in one.

He sighed heavily and leaned further into the railing. Being on 'their' balcony had always helped to clear his head, so he had persuaded his escorts to let him see the control room. They had talked to Sam for a while before John had asked to go to the balcony. Luckily, they let him go alone.

It was strange how their realities were so similar, the only differences being the people and Replicator situation.

It turned out that Elizabeth was now the leader of the rebel Replicator fraction, and was the go-between between Atlantis and the Replicators, she had also created a tentative alliance between Earth and the small fraction of Replicators opposed to Oberoth and the others. John couldn't help but be proud of her.

The event that had taken Carson's life in his reality had happened here, only, he had been further away from the explosion. He was injured, but survived to warn, mother and threaten his patients as usual.

John's grief struck him again and he bowed his head. How could things in this reality be so right, when his seemed so wrong?

"Hey," Elizabeth said gently, surprising him. He slowly straightened out and looked over his shoulder, smiling at her softly.

"Hey," he replied, turning to face the ocean again. He stiffened when Elizabeth joined him at the balcony, her arm almost touch his.

"Are you ready to go back?" she asked as she pushed some of her hair behind her ear. "Rodney says the device is almost at full power." She noticed John quickly turn his head and rested her hand on his shoulder, he shrugged it off and paced agitatedly. He stopped when he noticed her hurt look, and reached out to her, stopping midway and letting his hand drop. "John?"

He returned to his place at the balcony and gazed at the horizon. He heard Elizabeth sigh and shut his eyes tightly.

"Carson's dead," he stated intensely, finally meeting her gaze and holding it. Shock showed on her face as she gasped. She tried to speak, but John held his hand up. "In my reality Carson died in the explosion, there wasn't even a body left to take back home, just an empty coffin. His Mother cried on my shoulder."

"John…" she whispered, shaking her head and moving forward. "You don't have to…"

"We…I didn't go after you," he interrupted his voice cracking with emotion, even though he was incredibly still. He shoved his hands in his pockets and faced the horizon again. Elizabeth's hand gently rubbed his back and he sighed, leaning into her touch. "I wanted to, God, I wanted to. I even packed my gear up a few times, but I never did, and now your dead and I did nothing…"

"John," Elizabeth soothed, gently pulling in his arm to turn him around. "It's not you fault."

"Yes it is. I never should have left you behind in the first place," he snapped, angry at himself. And now your dead, and it…I" He stopped and breathed in deeply, closing his eyes and re-gaining his control. "Lizabeth…I…It's so hard."

Elizabeth's eyes shimmered brightly when he met them, and he watched, fascinated as a lone tear escaped and ran down her cheek. She quickly wiped it away before she spoke.

"Our realities seem so similar up until that point, I don't know if this will help at all, but…everyone else was told I was dead as well." John's head shot up sharply, hope shining in his eyes. "Teyla and the team she was leading ran into some clones of us, they were made to believe I was dead."

Elizabeth stepped closer to him and looked up into his eyes, folding her arms across her chest.

"John and Ronon weren't there so they didn't know and kept looking. It turns out the Replicators that saved me had faked all of our deaths to stop the others looking for us."

John reached out and gripped her hand.

"Maybe I'm on the same planet. I know it's a long shot, but if you want the co-ordinates of the planet then you can have them."

For the first time in a while John felt something other than grief and regret. It was hope.


McKay carefully handed the device to John and moved as far away from him as the room allowed.

"Rodney, what are you doing?" Alter-John and John asked together with the same expressions on their faces. Rodney ignored it all.

"I don't know what will happen once it activates, and I'd rather not be sucked into an alternate reality and suffer cascade failure," Rodney explained with a huff before turning to look at John. "Well come on then, we don't have all day."

John just shook his head as his twin groaned. He looked towards Elizabeth and smirked when he saw her smile. She mouthed 'good luck' to him before reaching for his doubles hand. His eyes widened in surprise just as the device changed shape, the pillar sinking inwards as a blinding light overtook him. Everything went black.

Slowly, he opened his eyes and found himself lying on the floor of Rodney's lab, the device just beside him. He blinked and when he opened his eyes again Rodney was above him, gazing at him in surprise. The scientist tapped his earpiece.

"Sam, I've found him," he reported, before turning back to John. "What happened? Where did you go? I told you not to touch anything!"

John barely heard him, his heart was beating wildly in his chest as he fumbled through his pocket. Then, his fingers found it and he sighed in relief as he pulled the folded piece of paper from his pocket.

He had a mission to complete.