At the end of season 2, Desmond turns the failsafe key. He goes into the "past" and buys a ring for Penny, something he didn't do in the original timeline. Eloise Hawking is there and she tells him he has to do what he always did.
It's my understanding that if she hadn't intervened, Desmond would have continued on a path that would have eventually enabled him to "let go" and move on to the next life. He would have died at that point.
Instead, he begins to remember and that he still has things to do in reality and the world collapses, he's returned to the real world, but now he's special because he came back from that place.
Remember that Desmond woke up naked in the jungle. Remember that when the smoke monster died it left a body - a second John Locke. It wouldn't surprise me if there is another Desmond, dead under the Swan.