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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.

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.

I would like to see a Daniel/Rodney/John. They are linked together by an Ancient device designed to mimic the wraith hive mind. Would really like to see the device give each of the guys one ability of the ancients. Maybe John has healing,Daniel has telekinesis, and Rodney has the ability to manipulate energy.Would really like it if you could include the following:Jack died so a grieving Daniel went on the Atlantis expedition,the Ori know about the Milky Way before they knew about it in Canon,they find Atlantis early than they did in Canon and the Ancients triggered the mind link device so the guys could protect the Pegasus galaxy from the Ori. Include as many characters as you want.

John/Nancy. Rewrite any episode to include a John Sheppard who is still happily married to Nancy, and she went with him to Atlantis.
Categories: Ship Pairings > Sheppard/Other Characters: John Sheppard, Other

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.

Sheppard's consciousness is destroyed, when that of an Ancient is placed into his body. There's no way to reverse the process, to remove the Ancient, and even if there was, John's consciousness has been destroyed. The Ancient formerly known as John Sheppard is just trying to fit in, not take John's place, find his own in Atlantis, but McKay is making things difficult for him though. Rodney Loved John, and he thinks that John loved him too, but they never spoke about it, almost never had to, because they were that close. Rodney hates this constant reminder of what he's lost, and he hates himself more, but he and the Ancient start a Relationship. At first it's because it's John's body, and Rodney can pretend that it's just sex, that it's sex with John, but it's not John, and Rodney finds himself in a Relationship with another man. He genuinely likes the Ancient, and together they're able to work things out, but the Ancient is on an uncontrollable path to Ascension. The Ancient ascends, but is able to return John once he does.
Categories: None Characters: John Sheppard, Rodney McKay

Rodney McKay is newly Divorced, and extremely wealthy, despite having had to force his now Ex Wife to take a settlement. The Marriage hasn't exactly ended badly, he doesn't quite know how he managed to snare Samantha Carter in the first place, it must just have been circumstance, but they're not close, and he's not sure that they ever were. Rodney is very high profile, having long ago abandoned the environment of a Lab, for an Office, and a portfolio of Government Contracts. That profile also puts him in a lot of danger, and he's been advised to hire a Bodyguard. He actually interviews several people, but what seemed like a good idea in his head, namely getting a hot, tall, blonde, female bodyguard, really doesn't sit too well with him in person. He never thought he'd say this, but his "type", just doesn't work for him anymore it's been spoiled for him, because it's as bad as if Sam were in the room, and what he actually ends up with is an Ex Air Force Major, called John Sheppard.