During his first year in the Air Force, the young and naive John Sheppard is propositioned by his C/O, and not feeling able to turn him down, begins sleeping with him. Somehow it's discovered, and John is Outed, despite the fact that he's actually Straight, but that doesn't stop him from being drummed out of the Service. However his C/O's involvement was never discovered, and with nowhere else to go, he takes John in, and for 10 years, John has been kept, as the now General's dirty little secret. He has no Life of his own, no friends, and is expected to cook, clean, and put out, he's always explained away being the General's Nephew, but he's the butt of a lot of jokes, and John hates the General so bitterly for the way that his Life has turned out. John is determined to get away from the General, and has been secretly attending University to get the Doctorates and PhD's, that he was never able to through the Air Force. One Rodney McKay is on a Lecture Tour at John's University, and he makes John laugh, something that he hasn't done that, they begin spending time together; and John gets his first friendship in 10 years. Rodney is working on Government Projects, and what neither of them know is that involves the red tape of having dinner with a certain General, something that is very awkward for them both during the evening, and after Rodney leaves, John and the General get into an argument, and the General tries to force himself on John, who for the first time, fights back, and it's also the first time that the General admits that he Outed John in order to get him thrown out of the Air Force. John leaves, going to the only person that he can of to go to, Rodney.
As Teenagers, John and Rodney were the Best of Friends, but what no one else knew was that they were also Lovers, but John broke Rodney's heart by joining the Air Force and leaving, without even telling Rodney what he was doing. John had 2 choices in how his Life turned out, he wanted to Fly, and Joining the Air Force would let him do that. He was in a unique position, to Marry a General's Daughter, almost through arrangement, a Woman he not only didn't Love, but didn't Like; or even find attractive. Or to admit to his Family that he was Gay, that he wanted to be with Rodney, the man he Loved, but couldn't bring himself to actually be with. John chose the outwardly easy option, something that has torn him apart through years of Marriage, but he's now Lt. Colonel, his Parents are dead, he and his Wife are estranged, and Divorce would be academic. He hasn't seen Rodney since he was a Teenager, but wants to try and find him. John knows that's it too late for them, he still Loves Rodney as much as he ever did, maybe more, but has to at least try to set things right. Rodney McKay works for the US Government, and John sets about trying to track him down.
John Sheppard has been escorted back to Earth, under arrest, and is being Court-martialled for having a Homosexual Relationship, the details of which aren't being made public. Despite Dr. Weir's best efforts, and argument that any such relationship should be excused for the good of the Atlantis Mission has been ignored, and John is to be Triad as if any other Officer in the US Military. Atlantis Personnel have travelled to testify for John, Rodney included, and who is absolutely livid that this is happening, he and John are Best Friends, and he doesn't know anything about this supposed Relationship. I mean, if any Guy were going to be with John, then it would be Rodney, but he never has been, and as close as they are, would either of them even want that? If John is found Guilty, he'll face a minimum of a Dishonourable Discharge, and a maximum of Prison, either wouldn't allow him to return to Atlantis, even as a Civilian, as the IOA wouldn't agree to someone with that that history, despite how valuable they might be. Talking to John in Custody, he wonders if there even was a Relationship, but is determined to find out the truth, if there was a Relationship, or is John has been framed, and then do whatever it takes to get John found Not Guilty, even if is means getting "Don't Ask, Don't Tell" finally abolished.
Sheppard has just seen McKay killed in front of him, he can't believe that it's just happened, and even visiting Rodney's body in the Infirmary doesn't make it real to him. Someone has to sort through Rodney's personal effects, and it's not fair the bring Rodney's sister to Atlantis, just to do that. John decides that it's something that he should do, as well as breaking the news of Rodney's death to Jeanne personally. During the journey to visit Jeannie, John reads Rodney's journal, and although he doesn't come out and say it, the way that Rodney writes about John, and they way that John feels about reading it, he knows that they had been in Love. Talking to Jeannie about Rodney, it's John that breaks down, admitting to himself what he couldn't when Rodney was alive. Now on the journey back to Atlantis, John knows that he can't do this without Rodney, he doesn't want to, and he's desperate to find a way to bring him back. SG-1 have brought people back from edge before, and even changed history, and John is willing to do whatever it takes to get Rodney back.
The worst thing that ever happened to John Sheppard, even taking into account his time in Afghanistan and the Pegasus Galaxy, happened when he was in his 20's, when along with his so-called friends, he participated in a Rape. Maybe that's the reason that even today, John can't commit to a relationship, because either the memory of that time comes back to haunt him, or the fear of what the other person would think of him if they found out. Now he's in a relationship with Rodney McKay, and what was the closest, most compensable Friendship, aspects that should have translated naturally into a Relationship, have made a painful, hate filled experience for John.
Not able to handle his feelings for Rodney McKay, or for their relationship, John Sheppard has an affair, well not an affair exactly because it's just sex, no better than what he's getting from Rodney, in actuality it's worse, but it's with a woman, and that's what John needs, to reassure his Heterosexuality, something that he's not willing to abandon. He doesn't want to be Gay, he isn't Gay, he just happens to have feelings for Rodney, and he likes to have sex with Rodney, but why does it have to be more than that. Maybe it is denial, but John loves women, and he doesn't want to give them up, even for Rodney. The problem is that Rodney catches John's indiscretion, and he's crushed, John does feel bad, and wants to explain that it doesn't mean anything, but also that can't say that it's never going to happen again. John's still not giving in to his feelings, and there's so much to work through, but now with Rodney broken-hearted, and distrustful, is that even anything that either of them want to do?
The worst thing that ever happened to John Sheppard, even taking into account his time in Afghanistan and the Pegasus Galaxy, happened when he was in his 20's, when along with his so-called friends, he participated in a Rape. Maybe that's the reason that even today, John can't commit to a relationship, because either the memory of that time comes back to haunt him, or the fear of what the other person would think of him if they found out. Now Rodney McKay is in that position.