I am starting to think that this entire thing will be a huge causality loop. It is probably going to turn out that the reason all this is happening is because of what is going on now. The people behind all this happening are Emerson's bosses. It might not be the case now, but in the future they determine there is a reason to do all of this, so they go back in the past... The reason the Alcatraz key was needed in the first episode is probably because they need it in the past to do something to make this all come about.
Not like Lost hasn't gone down that path before.