Disclaimer: All the characters and Concepts belong to their rightful owners and creators. Any alteration to existing characters or situations are my own doing, and I claim no profit from either. All song lyrics used at the beginning of each chapter belong to their rightful owners and musicians. No offense is intended in any alterations made by myself.

Rating: M

Warnings: Slash of the Mcshep kind, Mpreg, swearing and sensitive subjects, violence. AU, OOCness

Author's Notes: Normally I never would have thought that I'd actually write and post an Mpreg story, but this particular plot has been bugging me for weeks. This story is going to be a long one, so if slash, mpreg and long stories aren't your thing, then please turn back now!

In this story, Samantha Carter is the leader of the expedition and they haven't left the original home planet of Atlantis. Please note that there may be out of characterness for some characters, but in general I try to remain true to each character's individuality. I'm always open to suggestions, comments or constructive criticism, but flaming for any reason goes against the nature of this site.

Also note that I currently do not have a beta for this story, so there will be mistakes!! Feel free to point them out to me, and if anyone is interested in acting as beta to this story, I'd be very happy to hear from you!

Enjoy!

Prologue

May be surrounded by

A million people I

Still feel all alone

I just wanna go home

Oh, I miss you, you know

- Michael Buble, Home

It had taken Rodney years to learn that it wasn't ever one thing that made a relationship break. Usually it was lots of little things, mistakes and shortcomings, things that weren't said and things that were never meant to be said but were.

When his mother had walked out on his father, nothing had changed. Things had been broken between his parents for so long that he couldn't remember a time when they weren't. He had sometimes hoped that Jeannie wasn't as cynical about the whole thing as he was, but then again, how could she be? She had never had any trouble maintaining relationships, never had any trouble relating to people like he did.

So his mother had left in the usual flurry of drama that accompanied her wherever she went, and his father had watched as dispassionately as he ever had. And that, Rodney supposed, was why great minds could never live together peacefully. His mother had been an English professor, his father, a Physicist, and having two children more gifted than ordinary gifted children had possibly been a point of contention between the two. Having Rodney as a child obviously hadn't been easy on either one of them.

He had never quite been sure where he had gotten the sense that he was a disappointment to both of them. It was something he had always felt instinctively and had constantly tried to compensate for by being the smartest and the best at what he did. Jeannie hadn't seen it, nobody really had. It was just now and then, that he caught a glimpse of it in the looks, in the way they spoke to him. He had always been a little too independent for his own good, never wanting to ask for help, never wanting anyone to interfere with what he was doing.

Well, he definitely wanted help this time. Begged for it, prayed for it with everything he had, even if it was only in his thoughts.

After the first few weeks he stopped even that. Help wasn't coming, and it never would.

Atlantis was out of reach.

They asked him questions, endless questions. Where was Atlantis? Who was in control? How many soldiers were defending it, what kind of weapons did they have?

Rodney was only grateful that they didn't have the ability to probe his mind like the Replicators did because he always gave the same answers.

Atlantis was a figment of the imagination, a fanciful story told to amuse children before bed. A man named Spock was in control, and they had armies of killer rabbits and rag dolls. They knew his answers were false, he could see it in the calm serenity written on their faces, in the gentle smiles that graced their beautiful features, and he knew it would only be a matter of time before he broke. When the questioning was over for another day, he was returned to his cell, a lightless, windowless tiny room.

He didn't know how long he had been stuck in the room for, only that it seemed like unending years. It had probably been only weeks.

It always startled him, the darkness. Everything in their city was so pristine, so white and brigh, so shining and clean that it reminded him eerily of something he couldn't quite grasp anymore.

The cell was exactly ten paces across and fifteen paces long. At first he had used his hands to feel along the walls in the darkness as he counted each step from wall to wall but when he was sitting there with nothing but his thoughts as company it seemed so much bigger.

He was sure it was something meant to throw him off and drive him over that fine line that divided the sane and the insane. Rodney walked that line every day now.

The darkness became a kind of cloak. It locked the world out there and left him with his thoughts and questions and the tormentors that lived within his mind. He questioned every single decision he had ever made, he confronted all those bullies he had faced in high school and said the things he wished he had said to his parents all those years ago. It was too late now; they were both long gone, buried in the soils of his home world. He wondered what Jeannie was doing, how much Madison had grown, and if Caleb was still making that stupid tofu thing he had made for his one and only visit.

But mostly, he thought about Atlantis. He went over all the equations that made her work in those long dark hours. Remembered her soaring spires and the cool ocean breeze on his face, the quiet hum of her living and breathing around him and smiled when he thought about her temper tantrums, the warm comfort of returning to her after hard forages out into alien worlds.

What he remembered most vividly though, was the deep, sapphire blues of her skies. No doubt that would fade too, with time, but he was holding onto that as tightly as he could.

It hurt him to remember, stung like a thousand tiny little cuts all over his body, festered like a wound gone untended. He ached with the fever of longing to be back there, to see the faces of the people he had come to know so well in such a short amount of time. Close quarters and constant near death experiences forged bonds that were sacred, he had learned, and he hadn't ever wanted to see them severed.

And so while Rodney hated that darkness at first with a raging fire that had made him punch at the walls in desperation, it eventually faded into a dull ache, along with the rest of his emotions, and the darkness, oddly enough became the only friend he had left.

Soon even the memories weren't enough to keep him company or hold the chill at bay, and he was forced to live in the moment, moving for one hour of misery to the next. He grew tired of chasing memories that did nothing but make him ache. He was old enough to know better, and taunting himself with all the things he should have done wasn't going to keep him alive.

So one day, when a different set of guards came and collected him from his dark little sanctuary, he came to know a different kind of fear.

Yet a small part of him was glad for the change. He knew better than to struggle against the guards by now. Something in his being screamed out that he should, that he needed to but a new fear had griped him, all consuming and terrible in its power and he could do nothing but walk numbly between the two guards.

Because he knew what they were, and he knew what they were going to do with him.

It was their clothes that gave them away. Their spotless creamy white outfits were nothing like what the scientists back on earth wore, but the pristine gloves and goggles did.

The room they took him to was an unpleasant shock. A large box of plastic sitting within another room with a single perfectly made up bed, with one table, one chair and a small basin. It was like an observation room, and Rodney wondered, with a sick and all too familiar clenching of fear in his gut just what they would be doing to him now.

He came to know another type of nightmare which was so much worse than before. Days turned into a long, endless procession of dull routine. Rodney Mckay, once the observer had become the observed. He endured each test and scan in silence though, because screaming and fighting like he wanted to would do nothing but tire him out. He grew accustomed to long periods of obscure dreams and half conscious musings.

When he woke, he didn't know how long he had been asleep, only that he was strapped to a bed unable to move. A dull, aching pain existed somewhere deep in his belly, and his head was pounding like the after affects of a migraine. He lay there, taking in the plain white room, and found a feeling akin to weary amusement bubbling away inside.

Rodney should have been used to all of this now, but it still struck him as alien every time he really started to think about things. He had learned a long time ago that it was easier not to think, easier to just exist without that added burden, but old habits died hard and like everything else for him, Rodney's mind just couldn't stay quiet.

He lay there, awake and aware for what seemed like a year, but eventually, the dull throbbing of his body got the better of him and he slipped off to sleep again, wondering vaguely what he had to live for anymore if he was only alive in his dreams.

The next time he woke up, he was back in the familiar surrounding of his holding cell. He was lying on his bed once more, free to move, but he lay still for a long while, trying to figure out what felt so different and why.

Eventually, he moved, spurred on by the pain in his belly, and lifted his loose white shirt. When he found a long, thin red scar four inches long running the length of his belly he sat up, startled. They had done something to him. Cut him open and messed around with his insides. It looked like it had been done awhile ago, for the scar was mostly healed and there were no stitches of any kind, just the ever present ache..

Rodney leaned over the side of his bed and vomited the meager contents of his stomach onto the clean white of the floor before collapsing back onto his bunk, exhausted. He curled onto his side, hugging himself and wondered, for the millionth time, when the nightmare would end.

Things fell back into their usual routine pretty quickly. He was not harmed in any way, if you didn't count the daily injections and inspections and examinations. He sensed, somehow, that they were pleased. Whatever they had done to him, it had obviously worked, although he didn't feel any different, if you discounted the occasional ache in his stomach. There was no telling what they had done to him.

He spent inordinate amounts of time thinking of the possibilities of what they had done.

After yet another period of indeterminable time, something changed again.

The guards returned, bringing with them a syringe filled with that same milky substance. He sat still and let them inject him with whatever nasty drug they had come up with but this time they left him alone, and he flopped onto his back and felt that now familiar warmth spreading throughout him, the strange lights spinning interesting and lazy patterns around him.

A rippling shuddered passed over and around him, and he blinked lazily up the ceiling. Then the rippling came again, harder and he felt the floor shaking beneath him, and wondered idly if finally, finally the end of the world was coming and he was being granted release.

He closed his eyes and smiled, succumbing to the darkness willingly once more