On my news station, I get occasional short interviews with the shows producers. They claim that the two alternate realities that we are seeing are related to each other although how is yet to be determined.
If they set off the bomb in the past and the island is under water in that reality, does that mean that Jacob no longer exists there? Is that why other attributes of that reality are different, for example, Locke still being with Peggy Bundy and her speaking fondly of his father? What became of Christian's body?
Back in the alternate reality on the island, things are almost getting a mythology feel to the situation as far as Jacob vs the man in black/the smoke monster/evil john locke. At the temple, what is this darkness they speak of that infects Sayid and how does it relate to the black smoke? Is Claire also infected? In the previous seasons, was Christian "jack's father" an alternate form of the Black Smoke like Evil john Locke is now?
Who is the boy that evil john Locke spoke to, in the jungle? Was it jacob and if so, what does that mean as far as him being dead?