Sheppard wakes up, but immediately knows that something isn't right, he's not in his quarters on Atlantis for a start. On further investigation, he finds himself still in Antarctica. There was never any expedition to Atlantis, and taking his chopper out to the site of the Ancient outpost, find that there's nothing there. At least if the outpost is there, it's never been uncovered. John tries contacting the SGC, but it's not there either, the Stargate was never discovered. He sets about trying to find the others; Elizabeth is in the Middle East, negotiating peace talks, Aiden is in Iraq, John can't decide if that's still better than being MIA in the Pegasus Galaxy, and Carson he can't find head nor tail of. He's able to find out that Rodney is at Area 51, and knows that if anyone knows what's happened, and why John remembers, then it's his best friend. John doesn't have clearance for Area 51, but needs to get to Rodney somehow or other.
Major John Sheppard didn't go on the original Expedition to Atlantis, but a Year later, arrives on Daedalus during the Siege, and the first person that he meets is Rodney McKay.
Keller accompanies Sheppard's team on a mission, while McKay stayed on Atlanis to work on a project, but Keller is killed in an accident, and McKay blames Sheppard, who is destroyed that McKay would blame him.
John Sheppard is suffering from Post Traumatic Stress Disorder, it's been recommended that he return to Earth for recuperation, but he's refusing to leave Atlantis. Instead, he's asked for a leave of absence, and has moved to the Mainland, away from everyone. Rodney McKay however is not willing to put up with John isolating himself, and after a several weeks of everyone dissuading, and placating him, Rodney after him, but doesn't find who he expected to.
One word: Bubblegum. Do with it what you will :o)