Warped Mirror

Summary: When John Sheppard and Rodney McKay are drawn into a dark alternate reality, they've got to blend in to survive. There's more than it seems though and they may never find their way back home. Shep and McKay whump.

WARNING: This story contains mention of non-con, torture, graphic violence, and some minor and recurring character deaths, The story line becomes rather dark so be prepared.

Author's Note: This is an edited version of a fic I wrote a long time ago. I've always held a special place in my heart for this story and as such, decided to give it a tune up. If you haven't read this before, enjoy!

Prologue

"Ronon, Teyla, you guys through yet?" John kept the Jumper at a low altitude. If Ronon and Teyla weren't through the gate yet, then he'd swoop in to pick them up. Teyla's smooth voice came in. "Yes John, We have returned to Atlantis and are awaiting your Jumper and supplies."

"Come on Sheppard! I want my wine!" Ronon cut in on the radio, not caring who was listening in.

Rodney, who was seated next to Sheppard, rolled his eyes and spoke. "Oh, so I guess the Naquadah we're bringing back is nowhere near as important?"

"Nope."

"Settle down you two." John chuckled as he eased the Jumper forward, no need to go top speed. The radio was supposed to be for more official purposes but it's not like this was crunch time. "I got your wine Chewy and just so you know I'm taxing you half of it."

"I do believe I should try and be with my people tonight."Teyla muttered over the radio. "I foresee many headaches tomorrow."

The group had finished trade agreements with the people of this planet, colloquially named New Caprica as just like it's namesake in the reimagining of Battlestar Galactica, it was nestled within a nebula. The people were relatively friendly, but hesitant to trade with Atlantis. John had personally gone to negotiate, and after many tense hours of deliberation that nearly exhausted his reserves of patience, an agreement was reached. The Jumper's hold carried 400 pounds of refined Naquadah, as well as another 300 pounds of a random assortment of foods and drinks. They'd be back with medicines as well as an engineering team to improve the village's construction techniques and mining efforts.

"Lucky you Teyla, I'll tell you all about it when you get back." Rodney shot an annoyed glare at John. "Hopefully it'll be better than last time we partied on New Athos."

John rolled his eyes, and pushed the jumper away from the settlement. "Oh please, you cannot count that time. How was I supposed to know you had to dilute the stuff before you drank it?"

Ronon scoffed as he laughed over the radio. "Maybe when you started taking your pants off in front of Carter after the first glass?"

Laughter erupted over the radio; John cursed the eavesdroppers and decided to change the subject. "Err, yeah well, it was hot. And it's not like I didn't have shorts on underneath. 'sides; didn't you end up getting your hair done by Jinto and his girlfriend?"

Now even more laughter, John could imagine the look on Ronon's face and the beating he'd have to endure later in the sparring room. "Uhh, let's not bring that up."

"Gentlemen…" Finally, Woolsey's voice overrode any other laughter or banter on the channel. "…you can discuss each other's hair and trouser condition in private, please use the radios for official communications only."

John again rolled his eyes and kept quiet. While he did respect Woolsey to a point, the man's insistence on constant official protocol was a headache waiting to happen. During crunch time he knew his men were more than capable, but fun kept them in high spirits. He looked ahead to the landmass where the gate was and saw a bolt of lightning cross the clouds. "Rodney, that storm wasn't there an hour ago."

"What am I, The weather girl?"

"Thank heavens, no."

Rodney grumbled and pointed out the window. "It's a storm, nothing new."

"Is it dangerous?"

Finally Rodney began to work on the console ahead of him. John rolled his eyes, but paid closer attention. "Lets see, it's a pulse storm that's being created by the solar winds pulling the air in an updra…"

"Nyah!" John shirked his shoulders and turned to Rodney. "I didn't ask for its life story - Is it dangerous?"

Rodney made a similar irritated face back at John. "No no no, well… maybe, just keep us low and there shouldn't be a problem. Although…" He continued checking on the console, bringing up readings from the Jumper's sensors.

John kept the jumper at the low altitude with the trees towering nearby; he didn't like how Rodney ended his sentence. "Rodney?"

Rodney ignored him, and continued his scans. When he saw the electromagnetic field around the gate he murmured. "Fascinating…"

"Facinating?" John said. "What are you, Spock? Is it dangerous or not?"

"Figures you'd be Kirk." Rodney shook his head, but then clenched his Jaw. "And no, I don't think it's dangerous."

John didn't like that either. "You don't think? Rodney, we're carrying 400 pounds of potential high explosive – I need you to be sure." He began to consider backing off. Ronon could wait for his wine.

"Go! Don't worry about it! The jumper is shielded from electrical disturbances. How else does it fly in space?"

John clenched his jaw, and set the auto-pilot for gate travel. "Alright, if you're absolutely sure…"

"When have I ever…?"

John turned slowly and gave him the best 'you don't want to finish that sentence' look. Rodney silenced and looked ahead.

The jumper moved ahead slowly, and John kept his mental interface focused on the sensors. The slightest warning and he'd…

*WARNING, MAGNETIC DISTURBANCE DETECTED*

John reeled from the shock, the Jumper's computer was screaming it at him and even though he tried to move the Jumper away, the controls weren't responding. "Rodney! I've lost control! Something about a…"

"I know I know! I heard!" Rodney began to freak out as well. " Give me a minute!" His fingers flew across the console, trying to work some kind of workaround.

"We don't have a minute!" John looked ahead; the lightning was being attracted by the open gate, and bolt after bolt slammed into it giving off some kind of weird lensing effect. John kept trying to get the jumper to move off, but the pods had already retracted and the jumper was going through the gate. "We're going in!"

John braced himself for anything, and before he knew what exactly had happened, he felt the distinct feeling of going through the gate. Something was strange though, almost as if his entire body was flash fried and rebuilt differently. He didn't have a chance to think about it though, as he quickly lost consciousness.

"Sheppard! Lad, are you alright?"

John groaned, everything hurt, but that was a good sign, no spinal damage. The distinct smell of burning metal, smoke, and taste of blood in his mouth was enough to judge that the jumper had crashed. He didn't dare open his eyes yet; he always kept them closed until he felt everything else was ok. John could feel the pain fading already and muttered instinctively. "Ugh, I think I got whiplash."

A pair of hands came down on his neck, squeezing various parts and generally assessing him. "No, I don't think so."

"In my ass!" John answered bitterly with the reference, batting away the hands only afterwards realizing who he was talking to. "Wait, Carson?"

He opened his eyes and looked at a confused looking Carson Beckett, who with another 2 medics was pulling him out of the crashed Jumper. Everything had a strange darker hue, but it wasn't his eyes, the walls, ceiling, and even Carson's uniform were darker. He couldn't focus on his surroundings, only on Carson and his injuries. "Aye, your ass is looking pretty banged up, but you'll be fine in a wee bit."

John was feeling better, a lot better. Did Carson already give him a painkiller? "Wha… how… the hell are you doing here? I thought you were back on Earth." Before Carson could respond, John remembered Rodney. "McKay? Damn it, is Rodney alright?"

Carson nodded, but his face showed something strange, almost hostility. "Aye,Doctor McKay will be alright lad. Not more than a few bruises and bumps. He's got a horseshoe up his arse that one."

If John didn't know better, he would have sworn Carson spit at McKay's name. "The hell happened?"

The medics placed him on a stretcher, and a sudden bright light blinded him momentarily. John was still unsure of where the hell he was and his whole sense of direction and position was discombobulated. Carson's voice carried as he was moved. "Ain't it obvious? You crashed lad! Right through the gate and onto the stairs! Hell, you nearly flattened Chuck if he hadn't jumped out the way. I'd be peeling him up with a spatula otherwise." He finished on a humorous tone.

Thatgot John's attention. Carson was a Doctor first, and a dark comedian last. He'd never make a joke about someone dying. John wanted to say something, but now as he was getting his senses back to normal, he realized that he wasn't in his home.

The gateroom looked very different – dark banners flowed along like decorations, and marines manned machine gun emplacements as well as other strange looking weapons. They wore dark body armor with cables wrapped around them. John had never seen anything like it. They all looked at him with concern, but with an air of respe…

No… it was fear. For some reason they feared him. He could see it in their eyes. It was the same look Doolie Airmen gave Colonels and Generals.

The pain was almost gone; in fact John felt he could probably run again. Something was very wrong. He blinked away the pain from his eyes and looked around more. His suspicions were confirmed when Lorne walked up to him and saluted. "General sir, we received McKay's report on the depth of the Naquadah strain on the planet. Daedalus is standing by and Larrin is waiting for your order to deploy."

John did a double take. "Say again?"

Lorne got a worried look on his face, and he pulled Carson over from another stretcher. "What happened to General Sheppard? He's acting funny."

Carson looked at John, and shrugged. "I'm not sure, Colonel… until I get him under a scanner I can't tell for sure. Perhaps some memory loss."

John became indignant. "I'm acting funny? Since when am I a General and you a Colonel? And Larrin, on Daedalus?"

Lorne raised his eyebrows in shock, and muttered softly, but John was still able to hear. "We do not need this right now Doc. Fix him. I don't care what you have to do just get it done." He turned away and hit his earpiece. "Commander Larrin, You have a go for orbital bombardment. Commence resource extraction."

John tried to get up, but a pair of sentries who seemed to come from nowhere held him down as he yelled "What? Orbital Bombardment? The hell is going on?"

"Get a hold of yourself lad, you're just confused." Carson got closer, and the smile on his face made John suddenly fear what was happening. "Here." Carson flicked out a large syringe. "This'll calm ya down."

Despite fighting back, John felt the small injection into his thigh, almost instantly he felt the sedative begin to take effect, quickly losing all feeling in his legs. Before he could really argue anymore, the lights faded, and he drifted into a dreary sleep.

-Chapter 1 - Disbelief-

"Sheppard! Sheppard wake up! Damnit wake up soldier!"

John groaned again, the trailing effects of the sedative Carson had given him was wearing off quickly, but he still felt the dryness in his mouth, and the crusty material on his eyelids. "Rodney?"

Now he felt the trembling, Rodney's hands were shaking him awake, almost desperately. "Yes! Come on, shake it off!"

John did not like getting woken up like this. His brother David had once woken him like this after a night of drinking and John had thrown a full force punch. Dave's nose never did completely straighten after that. "Stop, stop it! Dammit McKay let go of me!"

He opened his eyes, and rubbed away the hard material that had caked onto his eyelashes. He was in the infirmary on a bed, but still in his BDUs thankfully. He felt stubble on his face and wondered how long he'd been out. John looked to McKay and instantly recoiled at how different he looked. "Jesus Rodney, the hell happened to you?"

Rodney was standing in front of him, with a massive scar running along his face from the left of his chin to his right eyebrow. Most of his hair was missing, and his complexion was terrible. He was a lot skinnier as well, almost emaciated. "I'm trying to tell you! Dammit Sheppard this isn't our Atlantis!"

John rubbed his face and recoiled away in surprise. Instead of his stubbled face he expected, he felt a distinct trimmed beard and mustache coating his chin. He shook it off and looked around – the whole infirmary looked strange, almost overstocked and busy. Equipment he'd never seen before beeped and whined, but he needed to focus. Rodney grabbed hold of his wrist and forced him to look him in the eyes. Rodney's eyes… they were almost whited over. "Holy crap… where the hell are we?"

John looked around as he listened to Rodney. "I don't know, but these aren't our bodies either, you've got a beard and some kind of healing ability, and I'm… well I'm five minutes from a bad zombie movie!" Now looking around and examining the differences, he could see this infirmary was very different. There were more ancient devices around, and other technology John had never seen before. "This is crazy Sheppard. I don't know the full story, but Atlantis is in space!"

John sat up straight, and felt a strange tingling in his body. "In space?"

Before John could further question him, Rodney shushed him as Carson was approaching having heard the commotion. "Aye, good to see you lads up and about. Should have left a guard or two to keep an eye on you. I know you hate me house'o'horrors." Carson chuckled at John, but frowned at Rodney.

Rodney spoke before John, his voice a bit hoarse and forced. "Yes well… the General and I should be fine thanks to your quick work."

Carson scoffed, and rolled his eyes. "Oh don't bother kissin' me ass McKay; I've given you all the painkillers you can handle. Another month on the outside, and we'll be free of your pestering."

John couldn't even begin to comprehend. If the situation were any different, he would have thrown a punch in anger. "Another Month?"

Carson looked and John and sighed. "Aye lad, seems you've had a bit of memory loss. Our scans show no brain damage or any other injuries so I suggest you go back to your quarters and let the wee guys do their work in peace for a day or two, Colonel Lorne has offered to handle things for now until you're back in ship-shape." He looked to Rodney. "As for you, I'm sure there's something in your lab you can waste the last bit of your life decoding. You're cleared for duty." He turned around and walked away, John fumbling over his both kind, and harsh bedside manner.

John got up off the bed, wondering where all the nurses and his friends were waiting for him. Instead it looked like only a few marines were nearby, watching but not doing much else. Since when did the infirmary need guards? Since when had Carson ever let him walk out of here without a million tests and nurse and orderly support?

McKay limped over around the bed, John now realizing he had a cane. "I don't have any idea what's going on Sheppard, but I think we should play it smooth for now until we know more, everybody seems to hate me here."

John patted himself down, what had Carson meant by 'wee guys'? "Yeah… yeah I umm… Damn McKay, how do we get outta this one?"

Rodney shrugged, and winced in pain. "At least you're in decent shape. From what I can tell I'm in the last stages of radiation poisoning. He wasn't kidding about painkillers. I'm hopped up to my eyes on oxycodone." He had a defeated look in his eyes, John didn't blame him.

Taking him by the arm, John led McKay out, unsure of whether or not to help the suddenly frail looking scientist. More than a few people gave them strange looks, as if it was shocking that he'd help the injured man.

Once they were out in the hallway and alone, McKay began to explain. "It must have been that magnetic storm. Somehow we switched bodies with our counter-parts in this reality. Lorne said you went because you wanted to show that village why they should join us, but they didn't want to get involved. Guess it didn't work because Daedalus bombed what little defensive capabilities they had from orbit and just took what they wanted." He shook his head and looked shocked. "Apparently you took me because everyone else was busy with more important things. I don't even think I have a rank in the civilians…"

John again felt the beard on his chin, and noticed a small bald spot along the edge of his lip, almost definitely a scar. "Goddamnit… I'm Evil Spock aren't I?" He looked to McKay in horror.

Rodney on the other hand scoffed. "And I'm Trip from Enterprise! All I'm missing is a hot Vulcan sex slave!"

As if summoned, Katie Brown suddenly appeared at the end of the Hallway. "Rodney! Oh my god Rodney! Are you alright?"

John cocked his head to Rodney and clenched his jaw. "Careful what you wish for McKay…"

She ran up to them, and quickly took Rodney from John's arm. She seemed so worried over him, and quickly took care of helping him along. "I heard what happened! It's so lucky you didn't get hurt in the crash!"

Rodney scoffed, but gladly accepted the help. "Yes well, Carson says I've got 'a horseshoe up my arse', and I'm beginning to think that's a good thing!" John couldn't help but snicker, though he still felt bad.

Katie wrapped her arm around him and tugged him along. "Come on Rodney, you should get some rest."

Rodney fought her off for a moment, and stared her straight in the face. "Just give me a second alone with Col… I mean… General Sheppard…"

John was nowhere near used to it. It had taken awhile to get used to "Colonel" Sheppard, General was a complete mystery to him. The look of fear in Katie's eyes at his words made John feel the need to reassure her "Yes… I promise I'll go easy on him."

Katie looked to John; again, the fear was there. For some reason John was feared on this base. He didn't like it. "Umm… Okay… please General…" She moved off, and quickly left earshot.

Rodney grabbed John by the sleeve and pulled him closer. "Listen, this place doesn't feel right. I'm sure you've noticed the huge amount of guards all over the freaking place. It's been almost 3 hours since Carson knocked you out and from what I've seen, we don't want to expose ourselves. They even had a team ready for cleanup of the crash, as if it's a normal thing!"

John shook his head, still confused. "Well if we tell them we're not the people they know, maybe they'll help us get back!"

Rodney's eyes said the whole story. "I was going to try that… but I don't think it'll go over well… Look at them Sheppard! Look at Carson; he hates me! I mean he'd probably kill me if he had the chance." Rodney looked intensely depressed; this reality had really kicked him in the stones. "I really think the only thing keeping me alive is you, Sheppard. They all respect you; I think they're willing to follow your orders no matter what."

Katie at the end looked down and spoke loudly. "Are you almost done?"

"Katie! I'm not done! Be quiet!" Rodney snarked; which John found offensive, but surprisingly he didn't feel like defending Katie, it struck odd to John that he would be so agreeable with this behavior. Rodney seemed to notice it too, and they gave each other a double take after a moment's pause. "Did I just say that?"

John nodded his head in confusion. "Yeah… the hell is happening? I should have smacked you for saying that… and where the hell is everyone? Where's Keller? And Woolsey? Ronon and Teyla?"

There was definitely something weird going on with his thinking, let alone his body and they just simply didn't have the answers. Rodney shook his head, unsure of any of those people. "I haven't seen any of them! It's just us; we're completely alone out here from what I can tell… Look, if this reality is anything like ours, there'll be information in the database about our history. Logs, people, planets we've been to – I can't access anything but my own research it seems, but you're in charge so you should have total access! You need to check it out Sheppard, and once we know more we can do something."

John scratched his head, god this was confusing. Rodney seemed surprisingly focused and even calm despite his circumstances. John was feeling strange, in a sort of nonchalant but fully aware mode. He knew he needed to get back, and that Rodney was going to get them back. But something was telling him no, that this was the place he was needed, and he had to finish a job here before he could go home. "Yeah… Rodney, what are the chances of us getting home? Be real."

Rodney sighed dejectedly. "Oh the usual, slim to nil. Once I start up my genius brain and get a look at the Jumper's readings I should be able to figure out exactly what happened and how to recreate it. I'm never wrong, remember?"

John scoffed, but again, it felt almost right for Rodney to be such an arrogant ass. "I think we should split up… Carson said I should get some rest, maybe I'll find something in my logs to help us."

Rodney nodded, and waved Katie over. She gingerly jogged closer, happy to take Rodney off John's hands. "Katie! We're done! Let's go!"

John watched as Katie took the abusive words from McKay with apprehension, as if scared to say anything just yet. SHe helped the now feeble scientist off. John stood there for a few moments before deciding to try and get some information. He grabbed his earpiece and tapped a com line open. "Ma… Colonel Lorne please come in." John winced, he would have to get used to this new higher ranked Evan Lorne.

"General? Is that you?"

"Yes… I think we need to have a little chat."

"Yes sir, I'm in Ops Center right now, we can talk privately in your office here."

"Uhh…" John pinched the bridge of his nose, slightly embarrassed. "Remind me where that is?"

"…The gate room, sir. The office across the control room?"

"Oh." John really felt lost now that he looked around. "Okay, I'll be there soon."

"Yes sir."

It was all so weird; Ops Center? His office? He'd always thought of it as someone else's; never having to be the big boss. It was Elizabeth's office… Sam's office and most recently, Woolsey's impenetrable fortress of boredom. John found himself wondering what decorations his counterpart in this reality put in it.

The journey to the gate room was quick, Atlantis still being the same design. Everyone he passed gave him a salute, some with a respectful apprehension, others with only fear. John tried desperately to convince himself it was the beard.

Once inside the Gate Room, Lorne quickly led him into the office. The gate room was fully staffed and teams were going in and out, much more so than his own Atlantis was used to. The gun emplacements and racks of weapons were the more disturbing part.

Surprisingly, a full door had been installed in the office and the glass windows had been coated over with a matte film. John looked around the office and instantly felt comfortable. On the walls, different pictures made neat rows. Some faces he recognized, others he didn't. All of them were from Pegasus, with only one distinctly being from Earth. He saw pictures of himself with Sam and Larrin hanging off his arms standing on the Balcony to the gate room with Ford and Lorne beside laughing, a picture of him and Sam standing in the back of a Jumper, posing in what seemed a intimate shot as she had her almost sad face on his shoulder, and still a last one with Teyla and most of the Athosian children gathered around John, a football in his hands and a giant smile on his face. These were only a few among more that featured various other worlds he recognized.

Most prevalent though was the one from Earth, it showed someone he hadn't seen in awhile. General O'Neill. But he looked different, instead of his traditional formal military wear; he had something akin to the same heavy body armor the Marines here on Atlantis wore. Even more, the picture showed O'Neill standing on a podium that distinctly said "Terran President." The bullseye drawn around O'Neill's head alarmed John, as did the darts stuck into the image.

Lorne must have noticed him checking out the pictures, as he began to explain. "Sir… I'm not sure how much memory loss you've suffered, but I'm hoping you still remember enough to continue our current mission. We need your leadership if we want to stand any chance against O'Neill."

"Against O'Neill?" John felt the lump in his throat grow.

Lorne sighed, and muttered to himself. "Goddamnit… you don't remember, do you?"

John turned to his XO, and before shaking his head, thought about it. "I… no… I don't remember, but I get the feeling it has something to do with him being President."

Lorne nodded, and clenched his jaw. "Yes sir. Maybe if we started with the last thing you remember?"

John considered it. He could tell him what he knew of his own reality, but by playing up the memory loss; Lorne might be able to fill the gaps. "It's weird Evan. I remember names, I remember places… but I don't remember any events… I think I'm gonna need a crash course on Stargate History."

Lorne made a slightly indecisive move with his head, and then nodded uncomfortably. "Uh… Yes sir, if it'll help…"

John noticed his reticence. "Something wrong?"

Lorne furrowed his brow as he closed the door behind him. "It's just… you haven't called me Evan in a long time… John."

John sighed, and sat down in the chair behind the desk. "I don't doubt it… It's not often I use it."

Lorne stood before the desk, and made a dejected sigh. "It's my fault, sir. We should have just taken what we needed instead of sending you to give them an ultimatum. I thought maybe if you showed up they might see it as a sign of respect and join up, but I guess they just didn't see reason. Larrin's got all the Naquadah she can hold already and she's heading back… I'm ready to receive any disciplinary action you may have for me."

John furrowed his brow, and contemplated what Lorne was saying. Is he saying I wanted to just blast that village off the face of the planet and take what I wanted? And i'm willing to punish him for not listening to me? The hell kind of man am I here?

"I should have listened to you, sir." Lorne continued. "This is war and we don't have the luxury of always being able to do things the nice way."

John didn't know what to say. All he could do was listen. "We'll see… just start from the beginning."

The beginning turned out to be almost 15 years earlier, during the original Abydos mission with Colonel Jack O'Neill and Daniel Jackson. It had taken longer in this reality for it to be concluded, as Ra had spent considerably more time torturing the survivors of the team for information. Colonel O'Neill in particular had gotten the brunt of it and nobody really understood how he coped. Finally after several months, the outcome of that mission was a fully loaded Goa'uld Mothership that then Colonel O'Neill managed to steal from Ra, having killed the false god in a long term plan.

The ship was brought back to Earth and studied, with the American government quickly reverse engineering many different aspects. It wasn't long before this attracted the attention of more Goa'uld and the Stargate Program entered full swing. The biggest difference was that the people of the SGC weren't the honorable people John was used to. Lorne told him of his own missions to steal technology while attracting the least amount of attention from the Asgard.

Over time, the Humans began to develop a serious power base in the Milky Way, The American government joined with the Chinese and British empires to lead the world in the Stargate program, giving their full commitment and resources to protecting Earth.

The Stargate program was made public shortly after the capture of Apophis and the subsequent publicly aired execution of said false god by new Jaffa allies. With the world turned upside down, religious extremism and smaller 2nd and 3rd world countries began a civil world war.

The military took over, and pretty soon the SGC became the sole unifying government. Things went on a similar note to John's own reality, as far as alien races and contact was concerned, up until the assassination of most of the command staff of the SGC in what was called a terrorist Jaffa attack. After this, Colonel O'Neill was promoted to the head of the SGC with his experience and connections, and soon after, unanimously voted to be the voice of the people in any off-world dealings.

Nobody knew exactly how it happened, but the Asgard had suddenly disappeared. O'Neill's first action was to sponsor an expedition to the Ida Galaxy and after a year, came back with all their technology and no idea where the Asgard had gone. Over time, it became clear that O'Neill had become a dictator, changed very much from the man John knew in his own reality.

John himself had been discovered through a military wide program to find people with the Ancient Gene. At first they thought he was just like any other, but soon it was evident his innate ability to control the Ancient Technology far surpassed anyone on the planet. His brother David had been checked as well, but only came up with a nominal strength gene. John was unique.

When the Atlantis Expedition was sent out, it soon became clear that this was yet another control that President O'Neill used, getting rid of all those with the Ancient Gene naturally and marooning them in another Galaxy meant that Jack would have sole control of the highest Ancient Tech in the Milky Way - just more evidence of the totalitarian state O"Neill had created beneath him.

Lorne stopped here, after almost an hour and a half of explaining. John couldn't believe it. But he was forced to pretend to in order to keep appearances up. "So… we're completely on our own then?"

Lorne nodded, and yawned. "Daedalus came a year after our arrival during the replicator Siege, and that's when we finally figured it out. You led the revolt and I followed. O'Neill is a madman and he doesn't deserve our respect, or loyalty."

John gulped, 'Replicator siege?' He remembered his own version at that same time with the Wraith – losing Ford, and again the almost suicidal mission he embarked on. He wanted to ask where those people were… Most of all Elizabeth… maybe in this reality she was still here, or if not here, then back on Earth.

But it was getting late and he was getting tired. He figured his logs might have details on his own missions here in Pegasus as Lorne had given him only the most general of knowledge. "Well, thank you Colonel, I think that jarred some memories loose. If you'll do me the favor and stay in command till I'm back to normal?"

Lorne nodded, and scratched the stubble on his chin. "Yes sir. I'll remain on duty until you feel better, although the sooner you take control back, the sooner we'll be able to move ahead with our plans."

John wanted to know those plans, but he wasn't ready for that. He was still reeling from the shock of learning part of an alternate history, and his beard itched something furious. He dismissed Lorne and left for his quarters.

This place was insanity. Replicator siege? What had happened? Where was Sumner and Caldwell? How had Larrin ended up Commander of Daedalus? Where were the people he knew and loved as his family? Where was Elizabeth?

It was very strange to look out the window and see stars. He was so used to seeing the horizon that it gave him a sense of vertigo. It wasn't long before he ended up in front of his quarters, wondering what insanity lay inside.

He opened the door, and was relatively relieved that everything looked normal. Except for the extra space, and the computer console festooned with complicated looking equipment, they were the same as his old quarters.

He didn't bother with the lights, and took his shirt off. John looked at the strange uniform; it was black like his regular BDU's back in his own reality, but with different markings, and different insignias. The star on his shoulder pads indicated his rank… Brigadier General.

He still couldn't believe it. He still didn't have all the facts. Why had his counterpart decided to revolt and take this place by force? John was tired, but needed to know. He looked to the computer, and sighed as he sat down.

Logging on, everything was the same. His password, the background image of Johnny Cash's first album cover, and even most of the folder names. There were plenty of other new ones he'd never seen. But the one he looked for… Logs and Mission Reports… was still right where he thought it would be.

He opened it, and saw the same reports he'd filed before, except these were video files. That was different. He looked around and found a headset. He also noticed a small fridge built into the desk and opened it. Bottles of what looked like beer, water, as well as a few tupperwared meals were inside. Opening a bottle of what smelled like beer, he sat back and opened the entire folder of his first year here, ready to watch as many as he could.

Arrival to Atlantis – Day 1

"Well… this is the first log I'm making here. The lost city of the Ancients… it's everything I could have imagined and more. I've spent all day interacting with the systems and it's amazing, even though it's all in gibberish to me I can sorta understand what each system does just by feeling alone.

Sumner has made it clear that's the only reason I'm here. He still doesn't trust me. I don't trust him either, something's up and I'm not going to like it when I find out…

Evidently we're boned, but that was to be expected since we can't dial back Earth anyways. The Ancients who left this place figured they'd be back and left the damn city underwater! The shield surrounding this place is almost drained, and with our generators backing them up, we've got a week on the outside to find more energy sources.

Sumner's been busy setting up teams and he's put me on his along with Lieutenant Ford and Sergeant Bates. Ford I can stand, he's just a kid with a steady trigger finger. Bates is an asskissing sonofa… whatever. Not like I have much choice.

Dr. Weir and Dr. Beckett found a holographic emitter, some old Lady was telling them about the history of this place and how the 'Lanteans' got their asses handed to them by some 'enemy'. I gotta admit, I didn't like hearing that.

Well I've got to catch some rack time before the mission. Going someplace called 'Athos' tomorrow. Hopefully we'll find some Zero Point Energy Doodads or whatever McKay said they were called. Here's hoping this isn't my last log entry."

John silently sighed, it was similar to his own log he'd made years ago, but darker, and with more hatred in his voice. Something told him he wouldn't like where the rest of these went. The next log started, and he paid silent attention.

Atlantis Log – Day 3

As Bender likes to say, we're boned. Yesterday we found a village of people on Athos, and Sumner and Bates got on their nerves pretty quickly. Thankfully their leader… Teyla… was reasonable and I managed to talk her into not chasing us off.

She showed me an old cave while our guys explored, and I found an old necklace she'd lost… and that's when all hell broke loose. Teyla could feel as 'They' showed up. The Wraith, the enemy that defeated the Lanteans ten thousand years ago according to Weir. I wasn't there for the initial contact, but they grabbed Sumner and a bunch of others including Teyla with some scooping transporter beam.

Bates took one of those ships down, say what you will about his social skills, that couldn't have been an easy shot. The other two ships got away through the gate and Ford managed to catch which symbols were lit up. I figured losing my commanding officer on the first mission we were on reflected pretty badly on us, so once we got back to Atlantis, I got a heavy strike team ready.

The Wraith are something else entirely, Space Vampires? You gotta be shittin me, but there they are. Feeding on the 'life force' of humans. Fuckers are hard to kill, that ship Bates shot down? Goddamned severed hand tried to attack me. Talk about an Addams Family moment. Beckett gave us a little biology lesson and it basically amount to this. Shoot them – a lot.

Weir didn't want us to go, and McKay babbled something about permutations. Negative whiners. Weir came around though, and a little arguing got McKay to see things my way. McKay had also found a way to actually get the city to rise up out of the ocean, so that's one certain death problem solved. The air on this planet is so fresh…

…not like that Wraith planet. We went in using a Jumper. And McKay, since I know you're probably going to see this eventually, Yes, I know Gate Ship is more technical and sounds formal, but come on, it's a big puddle, and it jumps from one side to the other. That goes for you too Ford.

That thing is amazing, the mental interface lets me actually see the air and space around me in a full 360 degrees while being aware of it all. It's like nothing I've ever flown before. Doesn't make me a turkey sandwich though so I'm just a tad bit disappointed. Even the 302's are nothing compared, although they're still faster.

Once we landed, we moved in quietly. The ship had some scanner we're calling 'Life Signs Detector' for now that I used to track our people down. The Wraith had a big ass lab in the forest, and we got inside pretty fast.

I'll say this about the Wraith, they're monsters. Teyla was right when she said they're abominations. We lost 2 men in there, and uhh… apparently I woke up a whole lotta Wraith from some hibernation… but we got our people and the Athosians out.

We almost lost Sumner, Damn Wraith bitch was about to… *sigh*… thankfully I had a good shot – If I'd hesitated it would have been a lot worse. He owes me one but won't say it. Bastard. We got them all out ok and managed to make it back to Atlantis in one piece. Most of Teyla's people came too since Athos is probably high on the Wraith list of places to go.

Sumner doesn't really trust the Athosians, but me and Weir convinced him to let them stay for now. They helped us, and are willing to keep helping us. We're completely cut off from Earth and it's just us out here. Sumner put me in charge of the Marine Contingent, and also 'Atlantis Recon -1'… guess he does value me a little. I've got Ford, McKay, and Teyla as my backup. He wants us to explore and see if we can find any more technology, especially ZPMs.

That's it for now really. Weir promised to open that ridiculously oversized champagne bottle so I better go before it's all gone."

John remembered that night, and talking to Weir about having to shoot Sumner. In some ways it seemed his counterpart had it easier. He opened the next file.

Atlantis Log – Day 6

"It's been busy, haven't had any time to update this. McKay screwed up, again. But at least he pulled it through in the end. I gotta admit, I wasn't expecting him to do anything even remotely like that.

As far as shooting him with that shield on; I can't, nor shall I even attempt to deny that it wasn't great fun. Grodin had fun trying to punch him too despite the singed knuckles. Sumner still doesn't trust the Athosians, but for the moment it doesn't really matter. Now that that crazy energy mist creature thing is gone, we've got some semblance of peace on this base.

The Marines are restless, so I set up a little firing range for them. The braver Athosians along with Teyla started their training today, hopefully Sumner and Weir can see that they're more than willing to join us.

That kid Jinto kills me, half the world's best scientists on this base, and the kid figures out how to use the base transporters 'fore we do. Go figure. I love that little guy. Doesn't like football too much though… gotta remember to not mention hockey again.

We should be starting our exploration in the next few days. Hopefully we can find more ZPMs and get this place running at full. McKay might be like a kid in a candy store with all the devices all over the place. But I feel something… maybe it's just my imagination, but I feel comfortable here. Almost as if the city itself is welcoming me…

Well before I sign my own section 8, I've got to go to sleep. Teyla mentioned something about Banto Stick sparring tomorrow. By far the best time of my day is watching her move so… Yeah… Shower time."

John chuckled, and wiped the forming tear on his eye. It had been awhile since he saw Jinto, and he wondered how the young man was doing back in his own reality… or if he was even still alive in this one. The next log started, the time code was a day John would never forget.

Atlantis Log – Day 10

"I hate the Wraith. I hate Bugs. And I hate Kavanaugh. Sumner is acting alright and Ford's tougher than I thought. That. Is. all."

John smirked. Pretty much exactly what he had back home sans the Sumner. The next few logs were nothing interesting, more complaining about Sumner, 10000 year old plants, and dozens of other small things that weren't any real important information. He noted slowly that his logs got less and less cheerful, and more and more angry. His beard appeared about halfway through.

In fact, except for Sumner being there, just about everything else was the same. The children on the EMP planet, the uselessness of their ZPM, the suspicions put on the Athosians by Bates, the first encounter with the Genii… that is until the log about the events of the Storm and Genii attack.

Atlantis Log – Day 163

"The storm is over… and the Genii are gone. We lost 4 men yesterday, and Weir, Teyla, and McKay are all in the Infirmary.

Sumner gave me a field medal, Silver Star for valor… I wasn't expecting that. He said I saved the expedition, and maybe he was wrong about bringing me along… I'm not so sure.

I killed more than sixty men yesterday… I might not have seen most them, but I've got to live with that. The Genii hate us now, and Sumner thinks we should consider a pre-emptive retaliatory strike. As much as I hate to say it… I think he's right. We can't afford to fight on two fronts. McKay insists he can build a nuke for us if we can find some plutonium and some uranium. Or if it comes down to it, he can repurpose one of our Naquadah Generators.

Kolya's gonna pay. I swear it."

John stopped for a few moments, he'd been watching for almost 30 minutes straight and was getting sleepy. He wanted to see what led up the siege though and kept watching.

Unbeknownst to him, the door to his quarters opened, and a slender figure entered, seeing he was busy at the computer, she silently changed clothes before heading into the next room.

John was too focused on the next few logs, and how they were so different than what had happened in his own reality.

Atlantis Log – Day 220

"Nanites. Machines a millionth of a millimeter big. Didn't affect me in the least, but at least McKay got to prove he could overload a Naquadah Generator if he needed to.

Sumner shot down 'Lizbeth's opinion pretty fast. She's pissed I agreed with him. It all turned out okay in the end but I'm starting to second guess Sumner… He's more open now but there's… something. He's hiding something… I don't think him being friendly is… friendly.

McKay says there's more information on the Nanites in the ancient database. All we need's a ZPM to make up for the one that we pulled out last week to power it. The old ZPM's got enough power for one 5 minute dial to Earth, and we're saving it for an emergency. I get the distinct feeling I'd rather not know what the Ancients did with those little nanite bastards."

Atlantis Log – Day 225

"Sumner's lying. I can tell now. Chaya… she showed me. This is all going to end in a goddamn horror show and I can see it coming… Nobody really trusts me right now, I don't think that'll change until this is over. I almost… I almost wish I could stay with her. I know she wanted me to stay… but she knows I'm needed here.

I was wrong, a few people trust me… McKay… Teyla… Ford… and for some strange reason… 'lizbeth… This is not going to end well."

When it came to the log about the ZPM hidden and worshiped by the Brotherhood, John couldn't believe his counterpart's words.

Atlantis Log – Day 285

"I killed Kolya today.

When we took the ZPM a whole melee broke out, he tried to stab me but my vest blocked it… so I stabbed him right in the chest… it was instinct… pure gut reaction. Stab, twist, pull out sideways… I saw the shock in his eyes. His blood spewed all over my uniform.

Liz thinks I'm a monster, McKay says I only did what I had to, and the city thinks I'm a hero again. Ford didn't say anything… I think I might have scared the kid. Teyla's been quiet too. In fact she's pretty much stopped talking to me for anything other than official reasons.

Sumner says he's proud, but we can never go back to that planet. We stole their ZPM and now I've got to live with that decision. If this ends up writing history… then let history show that I did what I thought was right.

The ZPM is nearly full, we've got 1/3rd power to the city… and thanks to the McKay and the ancient Database, we know where we can get more.

Asuras… I wonder what we could possibly trade to them."

John froze. The Asurans. The Replicators. It was three years they were in Atlantis before they found them… This reality found them within a year. He ran his hand through his hair, and sighed heavily. Obviously they'd survived, but this might explain what happened to his friends.

Atlantis Log – Day 300

"Liz isn't back yet, and Sumner's getting worried. We contacted Earth and requested reinforcements. President O'Neill promised us as much as he could send on the Daedalus, new battle carrier. Supposed to have plasma weapons or something… sounds powerful but I'll wait till I see it.

From what I saw on that planet when we first showed up, we won't stand a chance against them if it comes down to it. Sumner wants me to make a plan to get our people back… I think he's trying to kill me since he doesn't want my regular team to go.

In fact, only people who naturally have the ATA gene are a part of my team… He thinks I don't notice, but Chaya told me to be careful. Here's hoping this isn't my last log entry… again… and if it is. Fuck you Sumner."

The logs ended abruptly, and the next one wasn't for another month and a half. John almost hesitantly opened it, fearing what might be on it.

Atlantis Log – Day 347

"They're coming. It's inevitable. McKay barely got us outta there alive… We lost Liz, we lost them all. None of them were left by the time we got there.

I'm different… they changed me. Carson says I'm infected with and I quote 'Galootin' Nanites' and there's nothing he can do about it since they're holding me together.

Sometimes I wonder if he's a sadist, but he's always kept us alive. McKay explained it better, they were going to make a complete digital copy of our bodies for reference into their own plans… but they weren't all united. A replicator calling itself Niam… he let us go after a month of that hell.

Sumner's relieved me of duty. Teyla's come around and been a big help. Ford's taken over for me until… well we'll see what happens with these nanites."

John looked down at his hands, and instinctively pulled out the small knife attached to his thigh, he used the razor sharp edge to slit his finger open, and moment after, watched as the nanites healed the injury. "Oh my god."

A voice came from behind, it was soft and feminine, and completely unexpected. He turned suddenly and dropped his jaw in shock. The knife fell to the floor with a clatter and slid under the table. The gorgeous blonde was wearing nothing but one of his longer shirts, she stood in front of him and spoke softly as she moved forward to hold his shoulder. "I just got back, I heard you had a little accident. Everything alright babe?"

John finally managed to swallow the lump in his throat. "Sam?"

Sam wrapped her arms around him and brought her face close to his, she was wearing her long hair in a barrette that covered his face as she nuzzled him. "Carson said you had some memory loss… I'm glad you remember me."

John couldn't fight the urge to flinch, and the words came out. "Sam… uhh… this might sound really really stupid… but… what are you doing here?"

He meant in Atlantis, and to an even greater degree, half naked in his quarters. The answer was obvious, but he didn't want to face it. Sam got a hurt look on her face as she crossed her arms in front of her in a defensive reflex. "John? What's wrong? Don't you remember?"

John backpedaled, his arms hitting the wall behind him. This was not something he'd been expecting. 'Sure I mean… Sam's great and all… but Lorne said she was with O'Neill for his whole taking over the world thing… The hell is she doing here… With me of all people! ?'

"Umm… I want to say yes, but I'm scared to say no… So I'm just going to say, I have no clue what's going on, and I'd like you to help explain things to me."

Sam gasped and covered her mouth. "So you don't remember anything?"

John shook his head, and kept a polite smile, he wondered how silly he looked doing such a move with a beard. "Not a thing, but please, tell me." Her eyes watered, and she sat down on the bed. She was on the edge of tears and John had no clue why. His instincts told him to move forward, and carefully he sat down next. "Hey, look I uhh, I'm trying here. It's not like I'm not… I'm not against this Sam. I jus, I just don't know what happened to…"

Sam murmured. "For us to end up like this?"

John nodded. He'd been trying to go native with these people, but this was pushing the limits of what he called normal. "Yeah…"

Sam wiped her eyes, whatever the reason was it must have been something big. John turned her around and hugged her, trying to show he was comfortable with her even if he really wasn't. She reacted positively to that and muttered softly into his shoulder. "No wonder you were looking at your logs, you have no clue what happened." She waited a few seconds, and finally pushed off him. Wiping her eyes and the rest of her face, she quickly regained her composure. "Keep watching your logs… I'll be in the next room."

Sam got up, and despite obviously feeling terrible, moved towards the doorway to the next room. John got up and followed her hesitantly "Sam wait… can't you just…?"

She turned. "No John, I'm sorry I just… I can't. just please, please just, just finish watching your logs. I'll wait for you, I'll wait in the next room."

Sam turned, and almost ran into the next room. John fought his instinct to follow her, and instead just tried to comprehend what had just happened. And now for the first time, noticed something against his chest that had been dislodged by Sam's hugging. He pulled out his dog tags, and besides the 2 strips of metal with his military identity… was a silver ring. And now that he looked closer under the light of the computer screen, one of the strips was from her dog tags.

'Oh fuck me… McKay is gonna kill my ass."