Disclaimer: I don't own Stargate Atlantis, any of its technologies, settings, characters or plot lines and I'm only really borrowing one or two settings and characters for this anyway. Well for now. Who knows what will happen later.

Summary: John never had a family. He was military, raised from birth knowing what his future held. He was destined by politics to live with, protect and sleep with some genius scientist for the good of his country and all the civilians. What he never expected was to love or be loved.

Rating: M for slash

Kajos: Also a big thank you to cookie62 for being Beta for this.

JS had two years to wallow, two years to isolate himself from the world and his duty. After Nancy there had been a lot of talk of change, of reassignment and a review of his status. As it was he had been black marked and placed on helicopter taxi for two years. It was embarrassing, he was twenty, single and in Antarctica. Until the orders came through that an assignment had been found for him; news that he did have a life still. He was military and he was a trained special ops agent. Picked at the age of six with a high IQ and great potential he had been fast tracked into the select program that was reserved for this work. He had been introduced to Nancy at 14, they had had a year to get to know each other before they were married and Nancy was sent off on her first project. JS had gone with her, to protect her, as was his purpose.

He had failed. A year later it was discovered that Nancy had contracted a disease, it had made her sterile and resulted eventually a year and a half later in her death. Medical or not it was JS's fault. He should have at least made sure in the year that she had conceived a child; he had thought that they had time though. The letter was absolution. A second chance he had though impossible. Special ops were paired with geniuses at the age of ten; they chose special ops at the age of six when geniuses were selected from school to be certain that the numbers were correct. They were introduced at 14, married anywhere from six months to two years later depending on physical development and when they were sent on projects.

McKay though had gone through three SOs and sent them back. He was now twenty two and alone. Of course without special ops he was refused a place on any project. It just wasn't safe with his genes. The world was desperately streamlining population. In the early 21st century it had been realized that soon the world's population would become too large to manage. Countries everywhere had introduced various methods of population control. The USA and much of Europe had begun forced sterilization. Only those deemed to have superior genes were allowed to procreate. Only the top 5% of people in any area from field workers to politicians were allowed to procreate, those though were expected to have more children than was once the norm. To compensate for the effect of large families the civil service, military and education systems had been reformed. A pairings first child was automatically placed in the military where they were raised with the imbedded primary purpose to defend civilians and the country. The second child remained with the parents and third went into the civil service, trained from the start to be postal workers, lawyers, politicians, police or anything else the government required of them.

Other children if the parents wished could be given to sterilize couples the government deemed suitable. The system had pulled the world back from collapse but it had also cause controversy and war. Throughout the war geniuses, the best of the best were deemed as extremely valuable breeding stock that must be protected and utilized by each country. That was JS's purpose, to defend the countries best assets, the highly intelligent. He didn't know anything about this McKay other than the fact that he required an SO immediately and he was the only appropriate candidate.

JS landed in Colorado five hours after informing his CO in Antarctica he was leaving. A tired looking Colonel met him off the plane; he had to be at least 35. He checked his uniform and was surprised to see that the man was special ops and held a command position. It was unusual but not unheard of, normally it was consider risky, as you were required to protect your partner above all else.

"Welcome to Colorado Springs Major JS. I'm very pleased to see you."

"Colonel" He said and saluted. The man waved him off.

"Come on, I want to get you to the mountain as soon as possible. The good doctor is driving everyone insane."

"Really?" The Colonel looked JS up and down.

"I've read your file Major, you aren't one to follow orders blindly, you keep to your directive but unlike some you don't bow to the whims of civilians in your care. The last two SO's McKay has had were straight as arrows, boot lickers. They didn't do their jobs properly allowing McKay to get away with things he should never have been allowed to even consider because he told them to. There were five candidates this time. As the ranking SO I was required to make a choice, normal procedure would have been to contact the other four and give McKay the choice, you have a black mark after all. I didn't though. You were the only candidate that has any chance of keeping hold of McKay." The Colonel explained without hesitation. JS considered it. Nancy had often been care free with her safety forcing JS to act in her best interest even if it was against her wishes. "Now if you don't mind the car is waiting as is your scientist."

The journey passed in silence as JS catalogued his surroundings, noting every detail. He was already back in SO mode which Colonel JO next to him seemed to approve of. They arrived at the Cheyenne Mountain complex without issue. But JS was confused as they changed from the first elevator to a second that went down further than the lowest level of the known base.

"You are now entering Stargate Command. Better known as the SGC. We'll put you through the intro videos tomorrow, after you have met McKay. Just be aware that this is all above top-secret clearance. As far as any one you meet outside this base is concerned no matter what they tell you, this place does not exist unless, I or another confirmed senior officer of this command gives you clearance."

"Sir, why did McKay get rid of his first SO?" The Colonel looked at him.

"Because he was an idiot." The Colonel stated simply. This made JS gulp, SO's were the most intelligent members of the military, some were geniuses in their own right.

"Exactly how intelligent is McKay?" He tentatively asked. Nancy had only scrapped into the genius program.

"He's the smartest in his field they've ever had through the Genius academy." JS was stunned, geniuses that smart were celebrities yet he had never heard of the man in his life. "Don't worry, we snapped him up very quickly at the SGC making sure he was never known. His intelligence is as big a secret as this base." JO seemed to read his mind.

The elevator finally came to a halt and The Colonel exited followed by JS.

"Jack!" came a happy voice from down the corridor. JS stiffened as the young sandy haired man headed towards them down the corridor. He was clearly Colonel JO's partner, having used his first name rather than the initials that all military used both with one another and civilians. The man's face instantly brightened at his partner's presence.

"Danny." He said softly as the blonde reached them. "This is the new SO for McKay." He said taking the other man's hand. 'Danny' gave him a look over then held out a hand shocking JS to the core. He was a civilian.

"Nice to meet you, I'm Doctor Daniel Jackson. I wish you all the best with Dr McKay. He's…one of a kind. May I ask your name?" JS tentatively took his hand.

"Um…thank you. I'm Major JS."

"JS, excellent. Now I need to return to work. I'll see you later Jack?"

"Of course. I'll see you at six for dinner when you will be done for the day."

"Jack I have a lot of work to get through, I won't be that late, just this once."

"Ah! Six Danny. You're still recovering from that mission and none of that work has to be done tonight. It will all wait till tomorrow." The doctor acquiesced and left.

"I apologize, Daniel believes in military integration." JS nodded in understanding. He had never actually met an integrationist before though. He had always been aware though of those that disagreed with the fact the military unlike the civil service were completely segregated from the rest of society with separate shops, bars, restaurants and even a system of naming that separated them from civilians. Though JS could see their point, the military needed to be separate. They could not defend civilians if they were equal. Civilians always came first. If they made a request of you, you fulfilled it. It was not as though the military did not have rights they simply had a duty as well.

As they passed through the corridors JS quickly realized the unusually high prominence of SO's in the base. They seemed to make up about 50% of the military, this meant that the scientists and academics he saw with them and wandering the corridors alone were almost all Geniuses. What the hell was this place?

As they approached the lab JS could hear someone yelling.

"YOU INCOMPETENT BUFFONS! WHY MUST YOU TOUCH THINGS! I THOUGHT I BANNED YOU ALL FROM THE LAB! YOU'RE MAKING THE PLACE MORE DANGEROUS WITH YOUR INCOMEPTENCE!" The Colonel stopped and sighed as a small group of SOs left the room looking rather afraid.

"Those would be the dulcet tones of one Dr McKay." JS gulped again. McKay seemed to make him do that a lot and he hadn't even met him yet. "Don't worry," The Colonel said pushing him forward, "he doesn't bite unless you're withholding caffeine." JS slowly walked to the door and stepped inside.

"Whoever this one belongs to can you please teach him English? I told you all to get out!" McKay said. He was broad shouldered with a trim figure and a mat of brown hair on his head. His blue/grey eyes burned with annoyance but on first sight JS could see the slight bags under his eyes the slump in his shoulders and the twitchiness that suggested he'd been running on Caffeine for far too long. His brain instantly slipped into protector. He was pissed that no one had done something before now about putting a stop to this. "Hello? Anyone in there?" The Doctor said waving a hand in front of his face. "I told you to leave."

"Fine, I'll leave." The Doctor smiled. "As long as you come with me."

"What?" McKay asked wondering if this was a joke, he had important work to be doing.

"You heard me. Until you leave I am going to sit here and touch experiments and mess with things I shouldn't."

"And who would you be exactly?" McKay seethed.

"Major JS, Special Ops. Pleased to meet you." McKay exploded at that point.

"COLONEL!" The senior officer winced as he stepped into the room. "I should have known! I told you I explicitly did not want another watch dog." The military man straightened his back and starred back at the scientist.

"It's the law McKay and you know it."

"Oh, please. I am not procreating on the whim of some government policy. It's bad enough they force those operations on us."

"The Major is here for your protection as much as for procreation and you have already been told that you are free to make use of a surrogate as long as you donate your own genetics."

"How is he going to protect me? Is that thing on top of his head going to leap at the enemy?" JS was fed up now.

"I'm a fully trained SO, first in my class."

"Well that's good for you but I don't need a watch dog telling me how great I am."

"That's fine with me." JS scoffed. McKay starred at him indignantly.

"What's that supposed to mean?"

"Well, from what I've seen your just loud, that doesn't make you smart just annoying. Plus you obviously not smart enough to take care of yourself, it's been what eight hours since you last ate and you're certainly not getting more than a few hours sleep a night." The doctor starred at him in horror. "And I would say you need the sleep since you haven't spotted the obvious flaw in that calculation." He said pointing to a black board full of scribbled mathematics. McKay turned around and looked at it for a moment.

"No, those calculations are fine." JS just stood and walked to the board. He rubbed out a small section replaced it and then work through with the change. McKay considered for a moment, while Colonel JO grinned in satisfaction. He knew this would work.

"Now I think it's time we left and went somewhere a little less public for you to shout at me." After that the major just stood and waited in the doorway. After a few moments of stuttering McKay followed him out the door with JO bringing up the rear. They headed for the Doctors office as the closest place that was appropriate.

"Thank you so much for embarrassing me in front of my team Major, it really endeared me to you." Sarcasm poured out of the doctor's tone.

"I apologize but it was the only way to get you to listen." JS said seriously. "I'll be honest with you Dr McKay; this is not where I expect to be in life. You should know that I lost my first Genius. I allowed her to get a tropical disease because I failed to get her to see a doctor quick enough. She died. I never thought I'd get the chance to do anything important again. I am one of the best out there and I won't let someone I'm responsible for hurt themselves. As far as I'm concerned you are now in my care, whether you like it or not, you are going to eat and sleep more."

The Colonel cleared his throat pulling McKay's attention to him. "Do you accept Major JS as you're SO on a trial basis?"

"On a trial basis only, this is not permanent by any means." JO just nodded and left the pairing alone.

"Well, I suppose you should call me Rodney. What does JS stand for?"

"John Sheppard."

"Is John an assigned name or did your parents actually name you?" John shrugged.

"I thought you were Dr M R McKay anyway. What's the M for?"

"Meredith, but I order you never to reveal that fact." John burst out laughing.

"Meredith….Meredith? That's a girl's name!"

"Says the man who has initials for a name." John didn't stop laughing for a few minutes as Rodney snarked.

"Right, I think first stop is the commissary, then bed."

"Oh! You are not sleeping with me. I don't care what the politics say I'm not some stud to rut with anything that comes along with a hole."

"I wasn't even thinking it and anyway." He lowered his voice significantly "You're the hole here not me." Rodney just looked shocked and indignant, a look this John seemed to be causing a lot as the Major walked out the door.

After John had made sure that Rodney had eaten properly he stood and cleared both trays before returning to the table.

"Time for bed I think." He said smiling at the genius.

"Do I need to remind you that I am not sleeping with you?" The Canadian replied with a nervous confidence. John just rolled his eyes.

"I told you before; I don't want to sleep with you." He said standing and moving to the commissary door. "You coming." Rodney scrabbled out his seat and joined him. They set off down the corridor.

"So where is your room?" John asked suddenly curious.

"Oh it's the nearest one to the lab I could get. It's just the floor above next to the lift."

"Cool." The major said. They walked in silence for a few moments.

"So your last partner…"

"Nancy"

"Yeah, Nancy. Did you two… do you have… what I'm trying to say is…"

"We didn't have kids. We only really started trying just before the disease rendered her infertile. We were 17 we thought we had plenty of time."

"Good… I don't mean good that she was in fertile and died that is, just good you don't have kids. Not that it would be a problem if you did because you obviously didn't bring them with you. Wait that's not what I mean at all." JS stopped and put a hand over the doctor's mouth.

"I get what you mean McKay. You're glad I don't come with a load of extras that you'd have to get used to as well." Having finished he removed his hand from the doctors mouth.

"Exactly!" He said happy that the SO had understood his rambling.

"You do want kids right?" JS asked suddenly

"I don't know. I've never been with anyone long enough to consider it. I suppose passing on ones genes and wisdom to the next generation is a noble pursuit but I've never been inclined to miss that much work, I'm already behind on getting my noble prize by the time I turn thirty." He said waving his hands as though to emphasis his points."

"Noble pursuit?" John snorted. "I just wanna play with the little rug rats. Teach them how to throw a ball or surf." Rodney just stared at him in horror.

"There is no way any child of mine is surfing. Have you any idea how dangerous that is? Not to mention the extent of dangerous bacteria found in sea water." He starred at the SO who was grinning broadly, "Why are you so happy?"

"You just implied that we might be having kids some day." He said smugness evident in his voice, before he walked off leaving the doctor spluttering.

"I made no such implication. This a trial period only."

"You did."

"I did not."

"You so did."

"I did not!" The scientist practically squeaked.

"Deny it all you want but that was a Freudian slip which means you are interested in sleeping with me to have kids."

"I am not."

"See now you're just in denial"

"I am not."

"Are to."

"What are you five?" Rodney complained as they arrived at his room. "Anyway, this is my room so you can go away now." John shook his head,

"Not till I'm sure you're asleep."

"What you don't trust me?" The physicist asked indignantly.

"Nope, you've let yourself have as little sleep as you have. I'm making sure you lie down and stay down for a good twelve hours, even if it means sitting and watching you the whole time." The two men starred at each other for a minute before McKay relented; too tired to argue, the major was right, now he was at his room he really needed to sleep.

"Fine. But you better be quiet." He grumped before opening the door and stalking into his bedroom.

"I knew you'd see things my way McKay." He said following him in closing the door behind them. McKay changed into boxers and a t-shirt in the bathroom as well as brushing his teeth and using the toilet before emerging. John had taken off his jacket and boots before sprawling in a chair next to the bed.

"You're going to need to get a base uniform and go through orientation tomorrow." Rodney commented.

"Yep." The SO said clearly having thought of that all ready.

"Oh, well I suppose I'll just go to bed now then."

"Sounds like a plan." Rodney climbed into bed and closed his eyes before realizing he had left the light on.

"Ummm… Major would you by any chance mind…" The light turned off. Lord the man was quiet.