- Chapter 2 - Denial-

John realized that he only had one option. Watch the rest of the logs. Sitting down again, his fingers still going over the ring, he opened the next log.

Atlantis Log – Day 360

"They're here. The Shield is holding but we're still waiting for Daedalus. Sumner cleared me for duty so I could man the guns, but there're only a few drones left.

I've got to try, this is too important to be lost now."

The log ended abruptly, not surprisingly as they were under attack. The next log was almost a week later, and a lot bigger than most of the others. The image of the John making it was haggard, as if he'd been up for days.

Atlantis Log – Day 366

"It's been a year since I've been here, and so much has happened I don't know where to start. I guess I should start by saying this is the last log I'm going to make under the official chain of command. As of the end of this log, I am no longer a member of the United States Air Force. I accepted the rank of Lieutenant Colonel yesterday and am renouncing it today. I cannot in good conscience… or even alive continue with what I now know..

Daedalus arrived 3 days ago after some reinforcements through the gate 5 days ago, we've been fighting off assault after assault just barely. I've gotten no sleep since i'm manning the control chair. We even had to move Atlantis off the planet to get away from the Replicators. Daedalus docked, and their crew joined us in repairing and arming the city.

This is it, the moment Chaya told me I was here for, Sumner refused to move Atlantis back to Earth despite us being badly outnumbered. Even with the ZPM and Daedalus we don't stand a chance against all these Auroras they pulled out of their mechanical asses.

So I broke into his office, and I found it. I found the reason he won't take us back to Earth. It was hard to believe, but a few hours ago Lorne came to me and told me the same…

O'Neill's insane. He sent us here to die. He knew about the Wraith! Daedalus is here just to take the ZPMs, and any tech we've recovered so far. Then it'll just abandon us here to die. He doesn't want anyone who has the Ancient Gene naturally on Earth, he doesn't even care that there's a fucking gene therapy, he just doesn't want anyone to pass it on to their children!

Lorne figured it out when Caldwell ordered him transferred to Atlantis crew, he sweet talked their engineer Novak into giving him full access and found out. He's a natural gene carrier too and was going to get left behind as well. He came to me since I technically outranked him and told me the whole story.

He says that there's a rebellion building in the Milky Way, I'd never have believed it but Cam's gone AWOL and he's the presumed leader of the resistance, O'Neill's a dictator but no one on Earth can fight him since he's got the Ancient Control chair and Antarctica… He's got 4 ships in orbit at all times according to Lorne, no one can even take a pleasure flight without him knowing.

I don't have a choice anymore. Lorne's sworn himself to be loyal to me, and I believe him. The few people I've talked to are with us as well… they better be since they're natural gene carriers too.

We're gonna take Atlantis, Daedalus… and we'll see where we go from there.

I've said it before but I mean it this time. If this is my last log. Fuck You Sumner, and a big and definite Fuck You O'Neill, if I ever come face to face with you I'm going to tear out your heart with my bare hands.

John wasn't too surprised. From what this reality's Lorne had told him, John was pretty pissed off when he found out about the genocidal undertone of the Atlantis Expedition. Lorne hadn't been clear on exactly what happened that day, but the next log was a few days later, and looked equally large.

New Atlantis Log – Day 1, Day 369 in Pegasus

"We did it. I rallied everybody I could… even people who didn't have the gene wouldn't agree with them… We did it. In fact, just about everyone at and below Major joined us apart from the reinforcements from Earth.

Lorne led half our men and took Daedalus, he had Novak insert a virus to keep the ship crippled and show everybody what was about to happen. The same with Atlantis. Once everybody knew what the real plan was, people made their decisions.

We started the day with a total of 259 people on the Daedalus and Atlantis put together… there are a little less than 200 now. I don't regret doing what I've done, and I know there was no other way… and the only thing I do regret is that some of those dead had families, people who I've worked with for more than a year…

Sumner's dead… I went after him myself. He was waiting for me in his office… with a P-90E. He put two plasma bolts into me before filling my chest with lead. I should have died. I should had fallen to the ground and just left this place. Damn nanites kept me alive, but I felt every bit of pain… not something I'd like to experience again.

So instead I got back up, ripped the gun out of his hands, and dragged him to the Balcony. He begged me not to kill him. He begged me to let him go through the gate back to Earth and he'd never bother us again. He said he could serve as a one way messenger, to tell O'Neill about what happened.

I told him he didn't have to, because I was going to tell O'Neill myself… I threw him off that balcony, and he fell down and through the shield. No one saw me do it, but they all know I did. The only evidence is no one found his body.

Most of Atlantis command staff mutinied with us. I'm giving Lorne command of Daedalus for now, McKay found us a nice planet to land on so we can stop draining the ZPM with our shield. And we still have the list of gate addresses Elizabeth sent us from the past. With any luck we'll be able to hold our own for a good while.

Teyla doesn't know what to do. We can't dial in the planet Lantea anymore and we have no idea what happened to her people. She's pledged to help us as long as we take her people in… I'm going to do it. We need the crew.

Ford was with us too, but I think he's shell shocked. He got into a heavy fire fight with a pair of Marines from Daedalus and took a bullet to the leg and stomach. Carson says he'll pull through, but he still killed those two men at point blank range in anger.

I don't trust Bates too much, but I don't know what to do with him… it's not like he willingly knew about what was going to happen.

Carson didn't fight, but I can respect that. He might be a dark mother sometimes but he's honest. I'm glad he's decided to stay.

The others don't really have a choice… it's not like Earth will accept them if O'Neill's in charge… They're trapped just like we are. And they better learn to like it, because once we touch down, and get things settled with the Athosians… O'Neill's gonna get a little taste of his own medicine.

The Replicators have mostly stopped from what we know. Since we're their only target at the moment, they've retreated back to Asuras for the most part. A few Auroras are still looking, but finding one planet in a galaxy isn't exactly the easiest thing to do so we're safe for now. We're taking this break to regroup… god knows we need a little time to cope with this shit."

John wondered what his counterpart had meant, and also what he would do in the same situation. When Lorne told him about the orbital bombardment, he felt revolted. But if these are the things his counterpart had been forced to do to survive… No… not even all this would make him… John stopped thinking about it. He had to focus on the shattered woman in the next room. He had a feeling the next log would explain how she ended up here

New Atlantis Log – Day 8 – Day 374 in Pegasus

"Brigadier General John Sheppard…. At 38 no less. … If only it were official. After discussing it with Lorne, and the few majors left over from the mutiny…as well as the one colonel we rescued a few days ago… They've decided I'm the one they want to follow. Especially after our mission to Earth.

She should take charge... but she's in no condition to do that now. Can't blame her. At least she gave me an answer for O'Neill - the Sarcophagus. I can't tell anyone, it's too easy to excuse what he's done, but she explained what it does to a person's mind. O'Neill's not human anymore, he's a monster. I understand that now. Just another secret to take to the grave... if these nannies will ever let me get that far.

I miss Liz… the way she would argue with me and somehow make me feel better doing it. We never did find out exactly what happened to her. I'm hoping she's still out there… that somehow she got out like us. *sigh*…

There's so much to talk about… the last two days have been… unending.

Since I don't really report to anyone anymore, I'm going to be making this log more personal… if it wasn't so already.

Two days ago we raided the SGC. Using Sumner's IDC and a fake voice to get them to open the Iris… Me, Bates, Lorne, McKay and a heavy assault team of Marines went through. We moved in hard and fast and took the control room quickly. They all fought us… they all knew we weren't supposed to be there. I only recognized a few people, most of them new and loyal to O'Neill…

Maybe a year ago I wouldn't have thought twice. But after fighting the Wraith, the Replicators, and even the Genii… it's so hard to squeeze the trigger when it's an Earth born person. They didn't hesitate to try and kill us, so I'm not sorry.

The plan was to steal as many Naquadah generators and rare tech as we could, though specifically a new ZPM they found. With the control room, we disabled the self-destruct and locked down the base. I was hoping to catch O'Neill on a trip there, but the arrogant bastard was off-world on his flagship, Enterprise… pretty unoriginal name if you ask me.

We moved room by room, unlocking the base as we went. More of our men came in as we cleared the base, taking everything that wasn't nailed down. We aren't going to be heading back anytime soon, so everything counted, some of the more esoteric stuff were DVDs, books, chocolate… Hell I even snagged a box set of the whole Futurama Series plus movies and tossed it into one of the bags we were taking. It wasn't long before reinforcements from above started fighting us back. I still didn't know O'Neill wasn't there so I went ahead... nanites kept me going even as I took fire… I wanted to kill the bastard right then and there…

That's when I found her… I kicked in the door to his room and had the grenade in my hand, ready to pull the pin and throw. She was in the bed… the bastard actually…he… there weren't even any clothes in the place…! All she was wearing was a little… oh god…

John understood. His counterpart had found Sam on the base… in O'Neill's private quarters. The possibility of that happening in any reality made him want to vomit. He watched on the screen as his counterpart, the John Sheppard of this reality fought to keep control, finally showing signs of the emotional abuse he'd taken over the past year, moisture building in his eyes, his veins pulsing with barely controlled rage.

"… She saw me and didn't even scream, her eyes looked like I was some messiah come to save her. She begged me to take her, or at the very least kill her… I… I couldn't leave her there. Not with that inhuman monster. I had to give her my vest just so she… *gulp* *sigh*… the others were surprised to see her, but they didn't question it. They all knew what O'Neill saw in her, and probably guessed as much… she grabbed my pistol right off my leg and fought right by us. She killed 4 people that day.

McKay finally got what he was after, the new ZPM Earth had found buried in Egypt. From what we can tell and what Carter's told us, they were going to dial Atlantis and send a nuke through… guess we one-upped em there.. We switched out our old one with a minimal charge for that and dialed Atlantis. Carter even helped McKay set a Naquadah Generator to overload. As well as inputted her access code to reactivate the base's self-destruct.

We lost Bates, he stayed behind to hold off their main response force with his M249. I… I misjudged him. I'm praying I don't make the same mistake again. Since I'm a general now, I've given him a posthumous commendation, and dedicated the Armory to him… I think he would have appreciated that.

Even if they managed to stop one of the explosions, the other would level the place. We left with minutes to spare and we don't know for a fact what happened. But they haven't tried to dial into our gate, and we're not going to waste power by dialing them, so I'm assuming they still need to dig it out of the rubble – if it's even still intact.

Carter's in bad shape. Carson gave her a physical as well as a psychological exam and… *sigh* well…she's… it'll take awhile for the scars to heal. She's staying with me for now apparently… she won't stay anywhere else and doesn't trust anyone but me and Lorne for some reason. I'm more confused about me than Evan as they knew each other beforehand. He says he's never seen her like this and doesn't have anymore answers than I do. I offered her a room and a personal guard but… she insists on staying here with me.

McKay might be a problem since I know they have history, but hopefully he doesn't do anything rash since she's…. She's not normal right now, and if he tried anything I don't think she'd blink to kill him.

During the day, Sam's been helpful, she gave us a hand installing our new generators, and even streamlining some of our power systems. We've begun to arm Atlantis with just about anything we can, rail guns, plasma turrets, even some jerry rigged missile turrets the Daedalus was carrying. It's sort of a crime to turn such a beautiful city into a warship, but without drones, and no energy to power the other weapon systems, it's all we can do in case the Wraith find us let alone the Replicators.

In a way, the fact that she's here gives us an even bigger chance against any one of our enemies. She's had the most experience out of any of us and in many ways she should take command. Given the situation though, even she insisted I take over instead.

She… she cries a lot when she thinks no one's looking. I've caught her a few times already and she begs me not to tell anyone. I… I can't really do anything but sit with her and… I try and help but I don't have a damn clue what to do… how the hell do you get through to a… shit. To top it off I've been so busy lately she's taken to helping me get used to being in command… won't leave my side if it can be helped.

She's sleeping now… finally. She's been having nightmares and wakes me up in the middle of the night… I'd be wiped the next day but these nanites in my system are keeping me going no matter what, even though I look like the 7th circle of hell as Carson likes to put it.

In more official news, Daedalus finally made it to Lantea… they had to drop their own gate to the mainland to report in. Only about half of the Athosians survived. They hid in caves to avoid the Replicators, Daedalus is bringing them all back so they can be safe here.

Teyla has sworn her allegiance to me. Like she actually cut her hand and did a blood oath to prove that she's willing to die under my orders if it means her people will be safe… I'm glad she's sticking around since we're gonna need all the help we can get. But hopefully next time someone joins up I don't have to clean the floor of my office.

We need to start trading, and preparing for a long term stay in Pegasus, this planet we're calling "New Lantea" is off the main gate grid so we should be safe from the Wraith and Replicators, as well as those pesky Genii.

It'll be awhile before we can even think of going back to Earth. There's too many problems in this galaxy anyways to even consider it. At the worst we're stranded, and have to survive on our own, which we were doing already anyways. And at the best… Teyla says she's heard of other groups of people who resist against the Wraith and might be willing to ally with us.

We're going to one of those places in 2 days… Sateda… Hopefully we can get some kind of trade going with them.

This is Brigadier General John Sheppard… wow… that'll never get old… signing out."

John felt sick, the realization of what had transpired differently here than in his own reality… and the disturbing similarities was hard to cope with. Liz was still taken by the Replicators… Ford was still badly hurt during the siege… and Lorne had decided to stay. He still didn't know what had happened to Teyla or if he'd ever even met Ronon on Sateda… He began to understand why Sam was here, in his room, but seeing the large number of logs left, and the heavy weight of his eyelids, John decided it could wait till tomorrow.

He took off the headset, turned the computer off, and mentally prepared himself to talk to this alternate Sam. The lights were still off, and he kept them off even as he moved into the next room.

The darkness obscured it, he'd never seen a room like this in Atlantis before. John's eyes slowly adjusted to the lack of artificial light and he could make out Sam sitting on a chair a few feet away… next to a carriage she softly rocked. He couldn't help his throat clenching as he gasped. "Oh my…"

Sam turned and shushed him softly. She made a motion for him to stop when John went for the light switch. She was still sniffling softly and waved him closer. Her voice was barely above a whisper, just enough for him to hear. "John… did you see all the logs?"

John moved closer already feeling the lead weight in his stomach do flip flops. She seemed so perfect sitting there, gently rocking the crib back and forth… back and forth... "No, I uh… I stopped after the one where… where I talk about the raid on the SGC."

Sam took a deep breath to control herself. "So… you don't know about Evie."

John finally stood over the crib, and felt Sam's hand wrap around his waist, her head on his stomach. The little baby girl in the crib was sleeping soundly, a tuft of dirty blonde hair covering her tiny head. "Oh my sweet god… she looks just like you."

John knelt down, getting on his knees to inspect the child closely. Sam shifted her head onto his shoulder and held him tightly. "She's got your smile, and your innate ability of getting into trouble." Sam giggled softly as she whispered, the first sign that maybe she was happy.

John was shell-shocked; he couldn't completely register exactly who it was sleeping beneath his face. "This… this is our daughter?" He looked at the baby intently; he could see the mixture of himself and her in the chubby little face.

Sam rubbed his side, and whispered softly. "Almost a year old… our little miracle."

John still didn't completely understand. "Miracle?"

Sam pulled him away; he resisted for a moment, but then let himself be tugged like a disinterested mule back into the bedroom. Once she closed the door she looked at John in the darkness with her shining moist eyes. John couldn't help but notice how beautiful she actually was. "Yeah, she is a miracle." Her face shone with the smile he'd always secretly enjoyed, but only for a moment. "John, I'm sorry I freaked out earlier. Carson told me you were suffering some memory loss but, I guess I just didn't want to think about how bad it might be."

She moved in and hugged him tightly, way too tightly for anything platonic. He could feel her body pressing up against his, and despite all the confusion, all the downright insanity of the situation, he couldn't help but feel right. "Hey, it's ok. You have nothing to apologize for, if anything I'm sorry… I… I should have asked earlier if..."

Sam pulled him along again, and sat him down on the bed. "It's okay John… I'll help you through this. You don't have to rush into this… we should be okay without you for a few days…"

John couldn't take much more of this, he wanted to just tell Sam that he wasn't her John, that this was all completely new to him and he had no clue what kind of state Atlantis was in. But as he looked into her eyes, the pain hidden behind the joy of being with him and their… daughter… He couldn't bring himself to do it. Sam seemed so fragile that the thought that the man she had had a child with was gone seemed like too much a wound to give. "Yeah, I just… I'll watch the rest of my logs tomorrow and you can help me remember what's happened."

Sam nodded and brought her lips to his. Her tongue penetrated his lips and began to softly caress his own. A moment's hesitation and he returned the movements. John hadn't kissed anyone like this in quite some time, and he could feel the heat in her body as she unflinchingly pressed her body into his. Her hands slithered down into the back of his pants, and pulled the T-shirt he wore up and over his head. "I'll take care of you John."

John shivered, here was Samantha Carter, his old boss and most probable wife to General O'Neill in his own reality… undoing his belt and kissing his neck. All John could push himself to do was kiss her back, and rub her lower back with his hands as she began to tug his pants down. If news of this ever made it back to his reality, he was sure O'Neill would come down on him like a bag of hammers.

He contemplated praying for a miracle, since he didn't know if he'd be mentally ready for what this Sam wanted to do, and felt a sickening sense of relief at the sound of a baby crying. "Oh, I think..."

Sam stopped her exploration of his body, and sighed softly. "Yeah, I was hoping she'd stay asleep. I'll take care of her, go to bed John."

John thought about doing what she said, just sitting back and going to sleep. But now the sounds of his daughter… because she really was his daughter wasn't she? The same DNA, the same smile as Sam had said; so he shook his head and put his arms around Sam. "It's ok, I'll help – She's my daughter too."

Sam smiled, and made a soft noise of contentment; they got up together and walked into the next room to sooth the crying baby. John was at a loss as what to do. He'd babysat his reality's Torren a few times, but each time usually ended with him, Rodney and Ronon creating an unholy conflagration of chaos worthy of being called stoogely. John kept his arm around Sam as she picked up the child and gently rocked her back and forth.

All he knew right now was that even though this wasn't his reality, he could feel the sense of family with the people here. After watching the logs, the only thing he really found completely disturbing was their treatment of Rodney, even in his unbelievably frail state.

John was amazed at how maternal Sam was being, within minutes she had soothed the baby's cries, and with a little more comforting pats and rubs of Evie's belly, she fell asleep again. Sam set the child back down in the crib and rocked it back and forth again, watching the small child sleep washed away any stress John felt.

A few minutes later, John pulled Sam away from the baby, and getting back into bed, tried to keep his breathing and pulse under control as she cuddled up to him. Tomorrow would bring more information and with any luck, McKay would figure out how to get them back home, their home.

Evie had woken them up twice during the night, and John had finally begun to accept that he'd had a child with Sam, or more accurately his counterpart had. The nanites in his body kept him going though, and despite feeling tired, he now felt a bit more alert as he shaved… or rather trimmed his beard to keep the illusion that he was who he said he was. A knock at the door when he finished brought him out in his bathrobe. "Who is it?"

"It's Beckett! Get some pants on lad! I got no desire to see your bare ass anymore than I already have to! Least of all in the bright of the morning!"

John couldn't help but chuckle, and checked to make sure Sam was decent as well. He opened the door and saw the smiling doctor waiting with a small bag. "You make house calls now Doc?"

Carson laughed softly, and moved into the room without hesitation. "Just here to give the whole clan a check up. I'm hoping the wee ones have fixed you up a bit, 'else we'll have to figure out some other way of jogging your memory."

Sam had moved into the other room to pick up the baby, and John had a few seconds alone with Carson. "You could have told me I was married, with a baby in my room. I was in here for almost an hour before I even saw them."

Carson lost most of his smile, and got the caring apologetic look John was so used to seeing. "Aye lad, you'll have to forgive me for that. Usually the babysitter would stay until you came back but I asked her to leave before you arrived so you could have some privacy. It's usually been rather simple to treat you what with the little guys doing such a fine job." He set his bag down and pulled out a scanner. "If you don't mind? I'd like to see how they're doing."

John shrugged and stayed still, he felt a strange tingling sensation as the scanner's beam interacted with the nanites flowing through his veins. "Uhh, I'm guessing it's normal for me to itch while you're doing this?"

Carson nodded, and cocked an eyebrow at the readings "Aye, it's strange… the nanites don't seem to be in any sort of repair mode. I'd have thought they'd try and repair whatever damage is blockin' your memory. I guess Sam and… McKay… will have a bit of a day figuring out what happened."

Again, Carson didn't like even having to say Rodney's name. John wanted to ask what the matter was but Sam entered the room, and Carson quickly changed his attention as Sam smiled and spoke. "Good morning Carson, say hi Evelyn!" Sam grabbed the hand of the babbling baby, and waved it for her towards Carson.

Carson chuckled and moved forward to shake the baby's hand. "Well hello there little lass! How's our little troublemaker today?" the baby giggled, almost as if she understood what the smiling doctor was saying. "Sam, everything alright?"

Sam nodded, and sighed with a bit of dejection. "Yeah, You uhh… you didn't tell me how bad John's…"

Carson turned back to John, and sighed with his apologetic nature. "Aye… like I was just telling the General, I was hoping the nanites would fix whatever was ailing him, and I could keep from worrying you both more than necessary. But something else is up… so… I'm sorry Sam, but I'm gonna have to ask you to…"

Sam instantly became defensive, and looking away from Carson sounded bitter. "No! I'm not working with him! He can send me his data through the network but he's not coming within the same floor as me!"

John furrowed his brow. "Hmm? What's that about?"

Sam drew in a sharp breath, and her jaw quivered in rage. "Look John, I can understand why you kept him around, but don't expect me to just forgive him like that. Have him send me any data he gets and I'll do whatever I can for you. But I'm not seeing him again… ever."

John palmed his face and dropped his head. "I'm… not gonna like this am I?"

Sam sniffled again, another memory John didn't know about… and it seemed to hurt her to realize he'd have to listen to it again. "Carson, do me a favor and tell him. I'm gonna take care of Evie and Kevin with Lindsay today."

John might have heard it, but was still confused. "Uhh… Carson, I think we're gonna have to have a nice long talk today."

John didn't believe it. Rodney would never do that. "You are not serious. That's not the Rodney I know."

They were in John's office, all the doors were locked and the blinds closed. Carson had spent the last hour and a half telling John of all the differences in crew, how without the chance of returning to earth, people started pairing off since most of their loved ones were 3 million light years away. Carson had told John with a smile the way he'd announced over the PA one day that all military rules about fraternization were completely and emphatically flushed down the toilet – after standing in for a nice wipe.

Lorne had begun a family with Lindsay Novak, and Carson himself was dating a marine trained Air Force explosives expert, Captain Laura Cadman. Many others had paired off, but almost none of them had tied the knot like John and Sam had. In fact, as far as Carson was telling him, there were only 2 children on the entire base. John's daughter Evie, and Lorne's son Kevin, Kevin being named after a fallen friend. That didn't mean more weren't coming.

That was painful to listen to, Kevin Marks, a good friend of John in his own reality, a top quality pilot and gunner, and a man able to multitask like none other, had been killed by Steven Caldwell in the attempt to take over Daedalus. Marks had just seen the true orders the Daedalus had, and had turned to ask Caldwell whether such orders were truth when Caldwell had shot him point blank. Caldwell himself was later killed in a gunfight with Lorne.

In fact many of the people who John had come to support and expect to be there for him were gone, or had never even arrived on Atlantis. Jennifer Keller was a name that no one had ever heard, and Woolsey was just some political pawn in O'Neill's regime. It had all seemed so strange, yet somewhat believable until John asked about McKay.

Carson was telling him what made everybody hate Rodney despite his genius. "I know you were close to the man, and I even understand how you can look past it for our own good. But I'm not sorry he's dying, and I know Sam ain't either."

John felt his breakfast start to come back up, and keeled over from the shock. He held his stomach as he took short ragged breaths. "How did it… how did it happen?"

Carson sighed, and kept his voice low. "He'd been trying to make her feel better. Took her off-world a few times and tried to help her forget. He… he got drunk one night and tried to make his move."

John swallowed, more to keep his stomach to himself that anything else. "What happened?" He looked to Carson who noticed the rage in John's eyes. "Well don't just sit there, tell me!"

Carson smacked his lips, and leaned forward. "She was working on something in her lab, he came in and tried to get her to have a go with him. She'd… sorta been with you for a few months by then and he couldn't take a clue. The two of you were keeping it a secret. I don't really know why, you'd have to ask her. He tried to force her to go with him and they got into a fight." John kept quiet, and silently reminded himself that this wasn't his reality, and his Rodney would never have done such a despicable thing. "He got the drop on her since she wasn't expecting anything, but before he could do anything, Major Ford walked in on them and well, let's just say I let Rodney heal naturally to that one."

John rubbed his face hard, this was the most disturbing thing he'd ever heard. "Is that where he got the…?" he motioned with his index finger along his face.

Carson caught on quickly. "The scars? Nay, Ford smacked him up something harsh, but the scars were you, you lost your temper and well, you're not exactly the kind of man to piss off especially in those circumstances. When you were done, you told me to keep him alive, because we needed his intelligence if we were going to survive, but leave the scars to remind him of what he'd done.

"I told you then, and even though I've changed me mind I'll tell you again. I wanted to airlock the bastard. Or leave him on a planet with no DHD. But he's pulled a few rabbits out of his arse since… so I don't question your decision, sir."

John kept his breaths short, and he felt like crying. 'This isn't my world and this isn't my Rodney… Damnit… goddamn…' "How'd she take it?"

It was a rhetorical question, but one he still wanted the details to. Carson sighed again, the sad nature of the information getting to him. "She almost killed him. The two of you were together by then, and well… you talked her down. I don't know what you said, but whatever it was, it wasn't too much longer after that you both had your rings made." Carson sighed again, as if remembering. "He was my best friend General. And I didn't see it coming. I failed him, I failed you and I most definitely failed her."

John sort of understood why Carson hated the McKay of this universe so much now. An action like that, especially after what John learned everybody on this base had been through would be a harsh betrayal. This reality was so different, almost as if the thoughts and actions of everyone were amplified and darkened. He played with the ring on the chain around his neck and sighed. "When was that?"

Carson furrowed his brow, and cocked his head. "Ohh, bout a year and change after we took over. 2 years since in a few weeks. The Wraith were trying to hunt us down and he was getting really depressed. I know Katie's been taking care of him, and she still believes it was the wine that made him do it… but we were all here for him, and the poor lass had been through enough already. You really did keep her from losing her mind. I think your logs may say more on that than what I know though."

John unclenched his fist – when had he curled them? He saw his fingernails had cut into the palms of his hands, the cuts which now healed over quickly as the nanites did their duty. "Yeah, I'm not done reviewing them. Maybe I should and see what the hell I was thinking before I go and break his…"

John caught himself. Did he really just say he would go and shatter the bones of such a frail looking person? This was more that just trying to go native – something was pushing him to become more like the man he saw in his logs than retain his own beliefs, and if it was affecting him, it was most likely affecting McKay as well. He shook off the ire and looked to Carson who seemed to agree with his rough attitude. "I wouldn't stop you, sir. Breaking him I mean. But I do suggest you watch the rest of your logs, from what you've told me, you make a lot of em."

John nodded, and decided that he needed to talk to Rodney, now. "I think I might just do that. Thanks Doc… I get the feeling this is just one of many I owe you."

Carson changed from his serious expression to a weak smile. "Aye, but I reckon I owe you more. I'll be in me lab all day if you need anything sir."

John swallowed his rage, and nodded to Carson as he stood. "Thanks Doc, I will."

He watched as the Scottish doctor left the room, and left him alone to his thoughts. This reality was harsh, this reality was cruel. The people weren't the ones he'd become family to, and the family that waited for him in his quarters weren't his.

'Rodney… now.'

John got up quickly, and stormed out of his office. He looked to where Lorne was sitting at a computer panel and going over what looked to be munitions inventories. "Colonel, I don't suppose you know where Dr, McKay is?"

Lorne narrowed his eyes, feeling contemptuous at the name. "No sir, but I can track him down." Lorne opened a new program, and the city began to scan itself, he turned back to John. "You feeling any better, sir?"

John shook his head, and sighed. "Well, I feel fine, but I still don't remember jack squat. I've been reviewing my logs and Carson's been walking me through… certain events." John had a hard time repressing his rage. "I'm still not fully caught up, so I might need your help in getting completely up to speed."

Lorne nodded, and finally got a reply on his computer screen. "No problem, sir. We still have another 2 days before Daedalus comes back, I'll find some time to bring you up to date on our situation."

John raised an eyebrow, something he'd picked up from Weir. "Situation?"

Lorne nodded, and after pointing on the screen where McKay was, switched to a tactical overview of Atlantis. "Yes sir. Here's McKay in his lab, and about our projects…" He turned to John and gave him a slightly worried look. "Perhaps you should get caught up on what's happened in the past few years sir. We're a long way from what we started out with."

John grunted, but conceded the logic of it. "Alright… If you think that's best. Thanks again Colonel."

Lorne nodded, and gave John the same look of familiarity John's own Lorne often gave him. "No problem, sir. Get well."

John hid his surprise, it was the exact same look his own Lorne gave him when they showed the camaraderie they had. He quickly moved off, and found himself rubbing his chin with the neatly trimmed beard. Absentmindedly thinking what the hell possessed his counterpart here to wear such a ridiculous feature.

He moved through the corridors quickly, soon noticing things were very different than the Atlantis he'd come to know as home. Many of the balconies had been sealed off with airtight pressure plates, and those that weren't had heavy gun emplacements attached. Heavy gauge wires flowed all over the place, sending power to gods knew where.

Dozens of people walked by, almost none of them in typical Atlantis BDU's. A mixture of Traveler style clothes and a militaristic uniform were the predominant fashion. He recognized some of the people, but most were unknown Atlantis personnel he rarely interacted with. He'd noted earlier that on his computer was a complete list of crew assignments and bios… he'd have to take a look at those if he was going to be here for awhile. He saluted them all out of respect, and since they all gave him their distance.

It wasn't long before John reached Rodney's lab, which was devoid of the typical dozen or so scientists he'd no doubt be berating for any odd reason. Instead of finding him hunched over a tablet with a coffee mug on the table next to a ham sandwich, he found Rodney sitting and staring out into space – almost as if he were contemplating.

John found it difficult not to draw his sidearm and shoot the man. The bitter taste of what this reality's Rodney had done tugged hard on him, and he had to actively remind himself this wasn't the same man. "Rodney…"

Rodney turned, his face stoic and contemplated. "Sheppard… I've been waiting for you. There's a lot we need to talk about."

John fought to keep his voice calm, but the rage boiling in his veins showed in his clenched fists. "I'll say we do. Do you have any clue what your evil twin bastard did here?"

Rodney's face showed he didn't. "No... no one will talk to me. Even Katie won't tell me why. As soon as you walked away we started fighting. All I can access in the computer is my research. I don't even have any logs." He had a defeated expression on his face, almost as if he welcomed Sheppard's wrath.

John was willing to give it, and forced himself to back off, the strange pull begging him to act was overpowering, and he knew that if he didn't put some distance between them and his emotions, he'd most likely cave Rodney's face in. "You wanna know why? You really wanna know why everybody in this place would love to put a bullet in you?"

Rodney nodded, and looked to John with a gaze that showed his resignation. "No, but I have to know. I have to know what I did – why you've got a gun to my face."

John opened his eyes wide in shock – he hadn't even realized his right hand had already drawn the Sig Sauer P229. it shakily pointed at Rodney's head and John fought the intolerable urge to pull the trigger. At this range, the .357 SIG wouldn't leave much behind that could be called a head. He felt beads of sweat roll down his temple, and the vibration as his mind fought his body. "You… you…"

Rodney stared down the barrel, and John could see in his eyes that Rodney was ready to die, ready to pay the price for what his counterpart had done. "Yes…"

John bit his lip hard enough to draw blood; his mind was screaming to stop but his finger began to put pressure on the trigger, pushing the firing pin back millimeter by millimeter. Rodney closed his eyes and embraced the moment.

With a sudden scream of effort, John used his other hand to slap away the gun, it fired into the floor, digging into the alloy floor and sending up a loud spark. He dropped the pistol and felt the sudden release of tension, his senses finally coming back to him. John drew quick rapid breaths, falling to his palms on the table in front of him. Rodney cried, and keeled over on the desk sobbing uncontrollably.

A pair of marines whom John didn't recognize entered the lab with their weapons drawn, They quickly moved behind cover and screamed. "General! What happened?"

John was still in shock over nearly shooting his best friend. He turned to the soldiers and kept his voice low. "Get out."

The marines moved in quickly, securing the area and grabbing the loaded pistol on the ground. "Sir, we heard gunfire! Are you alright?"

John didn't like having to repeat himself, even in his own reality. The callous tone he used frightened even him as he used it. "I said get out! Now! Clear the area! Wait for my orders!" He snatched the gun back from the marines and holstered it, surprised at the violence of his movements.

The marines looked at each other, but then nodded and moved out. They got on their radios and soon John and Rodney were left completely alone. John looked to Rodney and kept his voice quiet. "The hell's happening to us Rodney…?"

Rodney sobbed, and as he drew short ragged breaths he tried to make sense of it. "I don't know Sheppard. I… It must have something to do with the body swapping. We've got our memories, but these bodies are used to a certain pattern, and that pattern is influencing us." He sat up, and using his cane to push himself along on the wheeled chair, sat in front of John. "I know I did something, something terrible. I've got the distinct feeling I should pay for it, but I think that's what the other Rodney thinks. He was ready to die and now I'm feeling the same."

John sighed even as his body quivered. He needed to tell Rodney what he'd discovered. "Rodney, the other Rodney… the one you say is ready to die…" he was silent for a moment, trying to build up the courage to say it. "…he tried to rape Sam." His tone went from a somewhat calm one, to a harsh and unsympathetic one.

Rodney drew in a short hard breath, and began to cough. His breathing struggled for a few moments until he finally stopped. His eyes watered uncontrollably and his voice cracked with sobs. "Oh my, Sam? She's on the base? I… I didn't… I've got… I have no clue about anything in this place! I… I mean… he tried to…?"

John felt the tears build up in his eyes too, but deep breaths, and the meditative techniques he'd learned from Teer helped to control his emotions. "Yes Rodney… that's why everybody hates you here."

Rodney leaned on the table, and was silent as he tried to fathom what happened. John kept silent as well, neither really knowing what to say. Finally, more out of needing to reassure himself than his friend. John spoke softly. "I know it wasn't you Rodney. I know you'd never do that. But this place is different. My logs are telling me how bad this place has gotten."

John stopped, Rodney needed to be his first concern, not the state of politics in this reality. Rodney sniffled, and wiped his eyes. "I'm dying Sheppard, I know Carson said a month but you can't imagine how bad the pain is. I can't even think straight. Katie has to help me with everything."

"Come on, what happened to the 'I'm always right' Rodney? You've gotta have some idea how to get us back!"

Rodney shook his head, and sighed heavily as he dabbed at his eyes. "I can't Sheppard, it's just too much. I was up all night thinking about it and there's only one way I can think of."

"What is it?"

Rodney palmed his face and sobbed softly. "We need to examine the Jumper, investigate that storm, and do a whole series of tests… the only problem is I'll be dead by the time we can replicate it, and the best person who I think might be able to help us would never help me here."

John winced as the realization hit. "You don't mean…"

Rodney nodded, his tone a quip. "Yep. I was hoping Zelenka could help but evidently he's not on Atlantis, he's with the Travelers teaching them.

John rubbed his eyes hard, he had to tell Rodney everything. "For the love of God Rodney, You don't even know why Sam's here…"

Rodney shook his head, but didn't face John. "No…. but I guess it's not good."

"Long story short, Jack O'Neill is insane and took over the SGC as well as Earth, He's using some weird Goa'uld sarcophagus thing, and it's affecting his mind. He sent everybody who had the ATA gene naturally here to Atlantis to get as much technology as possible before sending Daedalus a year later to kill us all. I didn't take too kindly to that and took over. We nuked the SGC in a raid and rescued Sam from him."

Rodney furrowed his brow, not understanding. "What? Rescued? Nuked? What the hell happened?"

John found himself feeling revolted again. It hadn't been him who broke down that door in the SGC, but the way he was feeling he figured it might as well have been. "O'Neill had her locked up in his private room for…" John couldn't finish and clenched his jaw.

Rodney on the other hand coughed once more, fighting back retching while John slowly told him everything that happened with just his movements. Having it all dropped on him like a bag of hammers was obviously not supportive of his mental and physical health. "Oh you're not serious… O'Neill? Those two are like soul mates back in our reality!"

John nodded, and sighed. "Don't I know it, and… you said these bodies are used to a pattern right?"

Rodney sniffled again, and winced from some unseen pain. "Yeah, I guess that's why I'm bawling like a toddler."

John clenched his eyes shut, and tried to make it as simple as possible. "Well, I think I know why I feel like I hate you. I'm married to Sam in this reality."

Rodney looked at John again, a mixture of shock, betrayal, and confusion. "What! But… how…? You know I…! Your evil bearded twin would have known…"

John huffed in amusement, at least the Rodney he knew was still somewhere inside this broken husk that sat before him. "We even have a daughter… I… I'm not sure of all the facts yet. I'm not too sure I want to know. So you might understand why I'm feeling reluctant to ask her to work with you."

Rodney nodded, and collected himself to speak. "I… I know… But she's the only hope I have Sheppard. The only chance I have of surviving long enough for her to figure it out is if you put me in stasis, and let her work on her own with the data from the jumper."

John sighed. "Yeah… I'm just not sure if can bring myself to ask her."