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.
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.
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.
When the Expedition travels to Atlantis, the Stargate Shield has been set only to allow Ancients to re-enter the City, only those with the Gene. Sumner and Weir never materialise, and the first person to enter the City with the Gene is Sheppard, others around him aren't being materialised, so John Radios for the SGC to stop sending personnel. Unintentionally, John is able to mentally deactivate the Shield, allowing one other member of the Expedition through, Rodney McKay, but no one else, and the Stargate shuts down. They're alone; and Atlantis' remaining ZPM doesn't have the power to Dial Earth.
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.