After their first encounter, the Replicators created their own versions of Sheppard and McKay. They have their Memories, and are trying to understand them. The Replicators run with John and Rodney's Feelings for each other, engaging in a Sexual Relationship. The Relationship was always there, and through the eyes of the Replicators, with no restraints, and no boundaries, they're free to explore.
John Sheppard is getting married, to a woman that his team rescued from the Wraith several months earlier. He's asked McKay to be his best man, but Rodney is being torn apart, he hates this woman, but she hates him far more, so far doing her best to keep Rodney away from John. Rodney is in Love with John, and at his bachelor party, tells him. John is angry, uncharacteristically furious, but the next day, they have sex together before the ceremony, but can either let the wedding go ahead now?
A hot-headed Major has just arrived on Daedalus; he's got an attitude, and a problem with everyone, but most noticeably a problem with Sheppard. Getting into an argument with John in the Commissary; he calls John a "Faggot", and "Colonel Cocksucker". Everyone is stunned silent, but no one more than John himself, he's Straight; and doesn't know where that's come from. The Major is sent back to Earth, and no one on Atlantis who knows John is taking it seriously, but Officers that don't know him are being overly professional, and the relaxed air that John has always liked to adopt is gone. John is feeling very self conscious, people aren't engaging him, women aren't flirting with him, and he's even sure that he's caught people laughing at him. What he can't work out is whether or not this Guy hit a nerve with what he said, did he know something John doesn't? John has never been intimate with another Guy, has never wanted to be, but now he's having to put up with what it would be like if he actually was, and he doesn't like it. John starts getting defensive, even with his Friends, and goes so far as to blame Rodney, thinking that maybe their Friendship is being misconstrued.
John and Rodney are Ancients living in Atlantis that is still residing on Earth. John is head of their Military operations and Rodney is working with Janus in the Sciences. John and Rodney built/build the Puddle Jumpers together. Rodney also creates the personal shield that was in season 1x3 Hide and Seek. Any additional expedition members are optional. I think it would be cool to have it end where Atlantis leaves Earth, since that is how the series starts, but that too is also optional.
When two Englishmen arrive on Atlantis, they cause quite a stir; they were married in a Civil Partnership, and the Military might not like this, but Atlantis is a civilian run expedition. One of the men is a Royal Air Force pilot, the other a scientist, and their relationship is eerily familiar, the bickering, and affectionate sniping echoing that of another pilot, and another scientist. People begin to talk about the extent of Sheppard's relationship with McKay. John is easygoing, but it's getting uncomfortable, and there really isn't anything going on between them, and he and Rodney are forced to examine their relationship for themselves.
So I had a thought. What if the Pegasus Galaxy wasn’t as accepting of homosexuality as it is normally portrayed to be? What if homosexual relationships were seen simply unacceptable in a ‘world’ where populations were small and the birth of children was necessary for the survival of a culture? I’d love to see a fic. where John and Rodney are lovers and somehow they are put in a situation where their friendship with Ronon and Teyla is questioned or destroyed due to the latter’s belief that such a relationship is disgusting, selfish, and possibly even criminal. Maybe their own relationship is revealed or possibly they have to witness someone being punished for being gay; noting that both Ronon and Teyla agree that the individual(s) deserved to be reprimanded/penalized.