This theory is based on the idea that once this is all over, you are going to be able to go back and rewatch the series and have a whole new outlook on the show.
This theory assumes the following:
-Jack ultimately takes the role of Jacob
-In at least one version of the future, something catastrophic happens in the real world future and this is caused by MIB. What's happening on the island is an attempt to thwart this.
I think the events on the Island have replayed themselves many times in the past. Some characters have seen the future or are aware of how things have played out. Certain things can change...but the "rules" govern that the past is what it is. You can't change that. Example: I think Ben may have been so sure his daughter was not going to get shot because he was aware of the "rules" and thought he knew how it would play out.
In what is a last attempt to save the world, a time loop has been created in an attempt to change what happens. This has failed in the past, but once the alternate timeline was created there was hope.
I believe when the time loop has played out in the past, MIB has won and escaped into the world - this is the horribleness that they are trying to advert.
Desmond is working to influence things to ensure the alternate reality becomes the new future. I think in all of the previous attempts to save the future, MIB has blown up the sub, everyone has died and MIB won and got out into the world.
But because of Desmonds influence on Said, things have changed and MIB still has work to do.
Jack will become the new Jacob and MIB will be entrapped in this infinite loop allowing the alternate timeline to continue.
When the series ends, Jack is now Jacob but the Island is also sent back in time for this all to play out again.
Thus, scene one of season one is Jack, flashing back to the plan crash as Jacob. Watching the first 3 episodes again I think it's very possible that there are two Jacks, two Locke's. The plane version and the "Jacob" / "MIB" version.
I think Jack quickly takes the form of his father Christian and ends up leading himself to water and watches over himself to influence events on the Island.
I know MIB said he was Christian, but it doesn't explain how Christian ended up off Island. It could be that MIB was using this information to manipulate Jack and gain his trust - obviously he can't be trusted.