It wasn't Rod that travelled from another Reality; it was John Sheppard's own counterpart. He's a pissy little bitch, Rodney McKay without the charm, and is somehow antisocial and lecherous at the same time. Not being in the Military, he's quite unrestrainedly Gay, coming onto every guy that he meets, and doing it in a clumsy; and offensive way. John can't stand him, and is both embarrassed, and angry at everyone seeing this version of him. He has a superiority complex; the man hates women, and even looks down on the men that he comes onto, seeing everyone as being below him intellectually. One person however catches Dr. Sheppard's attention, and he makes a play for Rodney McKay. Rodney wants to try and get to know this version of his Friend, but the play, and Rodney not immediately shooting Dr. Sheppard down, incenses John for reasons that he's not quite able to admit to.
When the Ancients returned to Earth, and evacuated the Pegasus Galaxy, they didn't abandon Atlantis, and were able to slip past the Wraith, and fly the City back to Earth. Once they had either Ascended, or Died, Atlantis was left abandoned, and the Second Generation of Humans on Earth, evolved with the City present in their History. Over time, Atlantis was entered, those that didn't possess the Gene could do nothing, but those that did, would use the Atlantis' weapons and defences for their own purposes. It was a point of contention, and cause of many Wars between peoples. Sat smack in the middle of the Atlantic, it has been in dispute for Years, with no one Country allowing another to occupy the City, but it is now under the control of an International Committee, lead by Dr. Elizabeth Weir. Carson Beckett is trying to find people with the Gene, and unexpectedly finds it in a Pilot flying personnel in from the Mainland, Major John Sheppard. Rodney McKay, who has been studying Ancient Technology all of his life, has been brought in from Area 51, and working with Sheppard, is be able to get access to Atlantis' systems. John and Rodney become quite the pair, exploring Atlantis, activating systems, and sometimes spending days entirely alone in the City.
I watched a beautiful fanVid, and i thought a fic would accompany it nicely. http://www.youtube.com/watch?v=Tv3zPl6t79E
Sheppard and McKay are dead, but they lived long enough to get married, not to each other, and to have a son each, they were the Best of Friends, and even named each other's son's after the other, Rodney Sheppard, and John McKay. Each son is the image of their father and with their mothers also gone they are now orphans, but are also now in their 20's. Although having been to Earth, they were born on Atlantis, have grown up here, and never joined the military, instead being absorbed into the civilian operation of the city. The difference between these boys and their fathers is that Rodney Sheppard has an aptitude for mathematics and science, John McKay fighting, and flying, and whether or not this is different they don't know, but they are attracted to each other.
John Sheppard and Rodney McKay are in Love, but they've never actually been able to be together, either one, or both of them has been with other people, or it just hasn't been right, but through everything, they've been Best Friends. For the first time, it looks like they might actually make it, but someone else wants to be with Rodney, and is willing to do whatever it takes to get him, even if it means hurting John. Rodney will do whatever it takes to keep John safe, even if it means sacrificing himself. "If anything happens to him, you won't see me for dust". "You get me for his Lifetime, not a moment longer". "If you die, and don't worry, I may want to, but I'm not going to kill you, and if he'll still have me, I want you to know that we'll be together". "What are you going to tell him?" "Whatever I have to, to keep him safe". Despite what Rodney says to John, John isn't willing to give up on Rodney, but the Mysterious Mr. X, is also not willing to make things easy, even if he does die.
Woolsey suspects that the good people on Atlantis are hiding something from him. He's right. John, Rodney, Teyla, Ronan and everyone else in the city are hiding John and Rodney's relationship from their new leader using lies, misdirection, acting, and a created crisis. Whacky fun ensues. In the end Woolsey does discover the secret (how is your call). Must include Woolsey remarking calmly at some point, "Colonel, you're out of uniform." to a naked Sheppard in the gate room.
The Goa'uld conquered Earth years before, and John Sheppard, and Rodney McKay; were taken as hosts. The Goa'uld were searching for Atlantis, and they found it, with John and Rodney being part of the group that travels there. Like any Goa'uld, they want power, and they want Atlantis for themselves, but they know that they need each other, John with the Ancient Gene, and Rodney with an inherent knowledge of Ancient Technology, they decide to work together to keep Atlantis for themselves.
Transported into the Past, John and Rodney become Knights of the Round Table.
Sheppard is returning to Atlantis, through the Intergalactic Gate Network and in a Jumper, but instead of arriving in Atlantis, he comes back through the Gate on Earth. His Wormhole hit a Solar Flare, and has sent him back in time almost 4 Years. He's surprised to find McKay at the SGC, this being before he was sent to Russia, and is even more surprised at how different Rodney is. Everyone is very suspicious of John, they've never seen a Jumper before, and are thinking that this might be a deception by Anubis. With Major Carter Offworld; it's down to Rodney to find John a way Home, and he does, but Orders come through that John is not to be allowed to leave. The Jumper is an important tactical advantage over Anubis, and both it and John are to be transferred to Area 51. John is being held at the SGC, and tries to get through to Rodney, tries to convince Rodney to free him; and to get him to the Jumper. Rodney does help him, but goes with John, he's already irreparably changed the Past; so what has he got to lose.
McShep. AU. Did anyone see David Hewlett in “Century Hotel”? I propose a WWII story with Sheppard as a flyboy and McKay – naturally – in Intelligence. They’re lovers, of course. First Time or Established, your choice. U.S. or Canadian, the consequences of being outed would be equally horrific. Only requirements: they’re lovers and they get caught. Bonus points for “rescuing” them (happy ending); negative points for using death as a way to avoid courts martial.