You know, it seems to me that Jacob’s role on the island is actually that of prison-warden: the Island is an elaborate prison housing the Anti-Jacob (whether he is a malevolent entity or an extraterrestrial). The Anti-Jacob can’t leave the island – Jacob can – and, as prisoner, can’t directly hurt Jacob: the prison itself prevents that, since he’s in the equivalent of deep lockdown. The Anti-Jacob can, however, obviously influence his other inmates, who aren’t bound by the same rules, into killing Jacob and opening up the prison.
I think this is important: the Island is Anti-Jacob’s prison, and Jacob is his warden. The Anti-Jacob can only escape the island if he destroys the prison or if he kills the warden. Either condition will do it.
Here’s where it gets interesting: both things have now happened, but in different timelines. Anti-Jacob appeared as Locke and manipulated Ben into killing Jacob for him in the “real” timeline. The prison warden is dead, and now the Anti-Jacob is going about affecting his escape. But in the new, alternate timeline stemming from the explosion of an atomic bomb at the Swan Station back in 1977, the island is destroyed. That’s his prison. The Anti-Jacob is completely free in that timeline.
So let’s ask ourselves a question: did the Anti-Jacob manipulate the destruction of the island back in 1977 just like he manipulated Ben into killing Jacob back in 2007?
I think he did: I think, just like the Anti-Jacob posed as Locke in 2007, he posed as Daniel in 1977. Think about it: Lost has reiterated over and over and over again that you can’t change the past. Whatever happened happened. All of a sudden, though, Daniel reappears after a mysterious three year disappearance to tell everyone that’s not true, and hey, blow up an atomic bomb at the focal point of the island’s energy and everyone will live happily ever after.
I think this is fundamental for how the season is going to turn out. Right now, the audience doesn’t really have any reason to care either way if the current-day Anti-Jacob escapes the island now that Jacob has been killed. Sure, he’s a bit of a dick, but why is it important for him to stay on the island? Lost needs to show why it’s important… and they’ve just opened up an alternate 2004 timeline in which the Anti-Jacob has been free for twenty seven years. They can use this timeline to show exactly why it’s important for the Anti-Jacob to remain imprisoned in the “real timeline.” My guess? We’re going to see the alternate 2004 timeline become an apocalypse really quickly.
I don’t know how it’s going to resolve: clearly, the main characters and their alternate timeline counterparts are going to have to come together to figure out how to keep Anti-Jacob on the island. But I think there’s a couple of clues.
First of all, Desmond is going to be key. Lost has made it a point to let viewers know that Desmond is special, in that he’s the only character for which Lost’s established time travel rules of “whatever happened, happened” does not apply. Both of his different timeline “selves” are going to be integral in bringing things together. My guess is Desmond is going to be the only character who is truly aware and in contact with his other self.
Second, Hugo sees dead people. Cool, but kind of redundant now that Miles is around, right? But a popular theory is that Hugo doesn’t see dead people at all: he actually is able to contact the counterparts of dead people who are still alive in another dimension. The Jacob who appeared to Hurley in 2007 may, then, be the other Jacob from 2004, who will guide the 2007 characters along in an effort to set things right.
Third, remember when at the end of last season, Jacob made a personal appearance to all of the integral characters of the show. He touched all of them. It was sort of a joke last season – Jacob shows up to hand Jack a candy bar, for god’s sakes? – but what if the point of that visitation was to make these characters aware of the fact that there are now two different timelines that need to be merged to contain the Anti-Jacob? Remember: Juliet was also visited by Jacob, and her dying words were to tell Sawyer that the time reset plan had worked… even though she had no way of knowing that it had worked/
These are just my working theories, but I really feel like the show is coming together. I can’t wait to see how the season progresses.