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.
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.