Sheppard has never been more embarrassed, he's contracted an STD, from an indiscretion off world, and it's highly contagious, he even set off Atlantis' sensors with it. Beckett has quarantined John off in his quarters, with instructions that he stay there for the foreseeable future. McKay can't resist visiting John; and takes great pleasure in teasing him. What he's not expecting is that his brief visit causes him to contract the same disease, and Beckett confines them both to John's quarters.
John Sheppard's Marriage was in trouble, and to please his Wife, he agreed to a Threesome with another man. John has never been with another man before, never wanted to be, and since he's in the Military, if anyone were to ever find out, the consequences would be severe. John's Wife is now using that threat against him, to degrade John, and force him to engage in further acts with men. John is miserable, and more broken than he could ever imagine being, made worse that one of the men that John's Wife brings home completely freaks at the prospect, and bolts, but when John bumps into that man, Rodney McKay, they've been left with enough to talk about, to be able to strike up a Friendship.
Working from the alternate dimension's Lieutenant Colonel Samantha Carter report, and now that Earth is protected from the Ori, the government feel justified in exploring the Pegasus Galaxy for technology to fight them with. Their only ZPM was depleted fighting the Ori, so are taking Daedalus to reach Atlantis. Everyone on the planet knows about the Ori, the Stargate, and the Ancient Outpost, but John Sheppard found out about it before most, when he had to fly Jack O’Neill out there, just in time to use it to save the planet! It's also there that John found that he had the Ancient gene, meaning that O'Neill could stay on Earth, and Sheppard could go to Atlantis. No one was particularly happy with that decision, but Carter's report said that Sheppard was already there in her reality anyway. In fact, most of the members of the expedition are those mentioned in Carter's report, those who are still alive anyway, and one of those members is Rodney McKay. It will take a couple of weeks to reach the Pegasus Galaxy, and Sheppard and McKay have nothing else to do but get to know each other.
John Sheppard and Rodney McKay grew up in the same small Town; they played together as children, went to school together, and finally fell in Love. John wanted to fly, something that the small Planes available to him, allowed him to do, but Rodney wanted to further his education, and that meant leaving, for a long time, and maybe never coming back, because an education wouldn't exactly be of any use in his Hometown. Rodney leaves, he leaves John, and then with a Doctorate, and PhD's in hand, does come Home. John hasn't waited for Rodney, he's gotten on with his Life, and their may not be a place in it for Rodney, and it may not be what either of them even wants anymore.
When the Expedition first arrives in Atlantis, and before the Failsafe was implemented, Sheppard and McKay are in the Jumper, when the City begins to Flood. They're transported back in time to when the Ancients still inhabited the City, both surviving the Jumper's crash. They remain in Atlantis after the Ancients evacuate to Earth, in order to sustain the City until the Expedition arrives. John and Rodney have barely said two words to each other, but decide to stay out of Stasis in order to get to get to know each other, and end up getting on each others nerves, but there's also an undercurrent neither is willing to admit to. Their next time out of Stasis, and they're pretty much unchanged, rotating the ZMP's, they know that this is going to be it for their Lives, and again decide to remain out of Stasis, this time around, getting very close, and going on to live their Lives together. Rodney and John are found in Stasis, John is unconscious, but Rodney is lucid enough to tell the story. Rodney also tells the other John and Rodney of his Relationship with his John, who also wakes up for long enough to tell his younger self that he loves Rodney, and also tells Rodney that too before they both Die. John and Rodney don't know how to act around each other, being told that in another time, you were not only in Love with, but spent a Lifetime with someone, does tend to make things awkward.
Sheppard, McKay, Teyla and Ronon are preparing to go Offworld, when someone comes through the Gate unscheduled. Rodney McKay comes through the Gate, and it is definitely Rodney, only he's much older. His Wormhole hit a Solar Flare, and sent him back in time; he explains that he just destroyed his Atlantis. The Wraith had taken the City, Rodney himself had been Fed upon, and it was the only choice, but throughout the meeting, this Rodney can't take his eyes off of Sheppard. John is made a little uncomfortable, and Future Rodney admits that his Sheppard was killed, but there's also something more. Talking to Future Rodney privately, he tells John that they had been together, and that his John had died saving his Life, had died saving everyone's lives. John is spending a lot of time with Future Rodney, it's Rodney, but he's tempered, the way he speaks to John, is so easy, and so comfortable, for both of them, and they get very close, but Future Rodney is Dying, and John is desperate to find another Wraith, to reverse the Feeding, like it was reversed for him. Future Rodney Dies, after an undisclosed amount of intimacy between them, John is left with things unresolved, and his own Rodney having been pushed entirely to the side throughout his Counterpart's visit.
This takes place after the events of Doranda. No one could easily forgive McKyy for what he ahas done with the solar system; and as such are making it so hard for him to be on Atlantis. Contemplating leaving for Earth, McKay does one last bit of rsearch with an Ancient device...that sends him to an Alternate Demention where his counterpart died, and all of the people on Atlantis icluding John Sheppard, Teyla, Ronan and Elizabeth are Ancients! Everyone in this Alternate Demension loves him, and everyone is unbelievably nice to one another. Weir, Teyla, and Ronan treats him like true family, and Sheppard, who has feelings for him, starts a relationship with him. All is too good to be true; so what happens when Rodney's own team from his Original Dimension comes for him?
John gets orders to be transferred out of Atlantis and Rodney realizes the only way for him to stay is to become a civilian. Unfortunately, John may be smart but he doesn't have a PhD and is therefore unqualified to join the scientific staff. So, Rodney offers to marry him next time they're back on earth so that John can come back to Atlantis as his spouse. This has to start out with them being best friends and SLOWLY falling in love through a series of steps and trials. I would love to see Jeannie helping them plan the wedding and the varied reactions of their friends and colleagues.
Sheppard and McKay are doing reconnaissance on Wraith movements, and have taken a jumper through a Space Gate, but heading back, something goes terribly wrong, and the Stargate is destroyed. They're nowhere near another Stargate, Daedalus in back in the Milky Way, is weeks away from Pegasus, and even further away from them. There are no inhabitable planets in the system, so they set course for the next, in hopes of finding one, but they're alone. Even if they do find a habitable planet, they're still going to be alone together, and right now, in a very small jumper, with very little food.