John's brother Dave has been brought to Atlantis, because he has the same Ancient gene that John does, and the same control over Ancient technology. John is uncomfortable when it's Dave that starts helping Rodney in the labs with Ancient equipment, essentially replacing him. The truth is that John liked spending time with Rodney in the labs, but becomes even more uncomfortable when Dave starts to replace John in their time spent together, drinking, watching television, and even just bickering. Dave is getting on well with everyone, but it's losing so much time with Rodney that really gets to him.
Pre-DADT repeal, any season 1 really. Lorne and Sheppard are overheard by a member of the Atlantis group who wants to get rid of Sheppard. However, he/she doesn't know who it was that Sheppard was with. Not wanting Lorne to be removed from Atlantis as well, Sheppard convinces McKay to go along with being his fake boyfriend somehow. Lorne's not exactly happy with that plan, but he is thankful. Eventually, McKay and Lorne are left on Atlantis, while Sheppard gets sent back until he can figure out how to get back to Atlantis.
Despite restoring him mentally, Dr. Beckett was not able to restore Sheppard's physical appearance, and he has remained in his Wraith like state. John has had to fight to continue to go offworld, especially given the reaction he receives from the locals, and ever since, people in Atlantis have been extremely uncomfortable around him, especially Ronon. Rodney however hasn't once treated him any differently, and it's such a contrast to John, deprived of even the intimacy of friendship. It's the only thing that he's got, but it's also genuine, and John is falling for Rodney, but Rodney is his friend, pretty much his only friend at the moment, and he doesn't know if he would want to be with another man, let alone a Wraith.
This story can have any pairings. However, the characters John Sheppard and Rodney McKay from the Dark universe must be together. The main point is the John and Rodney form Our universe tampers with some Ancient device that brings a Dark version of themselves, (and any other Atlantis character of your liking) to Our universe. The device they used allows their alternate selves to stay longer without any entropic or dangerous effects. You can have some minor or major event with the Wraith (or anything else) happen while the Dark Sheppard and McKay are there, so that the John and Rodney from Our universe can see how evil/dark their counterparts are. The dark counterparts can be civilised to eachother, or one more dominant than the other. Your choice! The number one rule...? HAVE FUN!!! ;D
Sheppard is being visited in the night, by an Ancient that stayed watching over Atlantis, and who has taken a shine to John. Appearing to him in his Dreams, the Ancient takes the form of McKay, and Seduces him. John is badly disturbed by these Dreams, not knowing that they're anything more than that, but takes out his frustration on Rodney, like he's somehow to blame. John knows that it's not Rodney's fault, they're his Dreams, and he's enjoying them, but Rodney's also not about to let this drop.
McKay is on the other side of Atlantis conducting repairs, when he's grabbed from behind and blindfolded. Rodney doesn't know who's grabbed him, or what's going up, until whoever it is rapes him. Rodney has never experimented, also never wanted to, and hasn't had to much as a suppository, or a colonic, but this is sawing his virginity out of him, and he never wants to again. When it's over, Rodney is dragged into some nearby quarters, and put into the Ancient shower, he's knows what's happening, that this won't leave any evidence as to who has attacked him. He stays in that shower, until someone comes looking for him, and that's Sheppard, Teyla and Ronon. They find Rodney is a terrible state, and all of them feel so helpless. Only the four of them, Carson and Elizabeth know what's happened, Carson has no physical evidence as to who attacked Rodney, and as ranking military officer, it falls on John to investigate, and he wants to find out who did this. What's worse is that Rodney can't help but suspect everyone around him, including John, something that hurts them both.
For the last couple of weeks, John Sheppard has been sleeping with Rodney McKay, only it hasn't been John, it's been a Goa'uld in control of him, using Rodney to get information to destroy Atlantis. When the Gou'ould is discovered and removed, John and Rodney have to deal with its actions, and what has been changed between them.