Faraday steps out of the sub in a badass new black Dharma jumpsuit, complete with ultra-top secret Swan clearance and ball-kicking confidence. This explains where he's been for the last long while (three years?) although it doesn't tell us anything about what he's been up to. Yet whatever that is, he's either crazy or stupid enough to drag himself back to the island. And so the big question: why?
As huge a proponent of the 'Whatever happened happened' theory Daniel's always been, I'm willing to guess he might've been looking for a way to change that ideology. The Daniel who left the island was a gibbering, resigned, broken man. The guy who steps out of the sub looks newly confident and ready to rock. Just like Benjamin Linus, I think Daniel is now prepared to fight the inevitable. Whatever he did in Ann Arbor, it probably involved some rats and some mazes and some insane mathematics. I'll bet he came back to save his friends, but mostly to save one other person from the inevitable: Charlotte.