Lost Thoughts
Ok, so a long time ago (I'm talking hundreds maybe even thousands of years ago), Jacob and the Man in Black were on the island and resided in the Temple. I believe there was someone else on the island also, a power that was greater than both of them and was the true ruler of the island. More on him later though.
So Jacob and the MiB perhaps are rivals for the next true leader of the island, but they have differing views as to whether people can be trusted to come to the island, or if they will just corrupt and exploit it.. Jacob believes in the goodness of man, and the MiB believes that that man is corruptible. Through this argument, they are removed from the Temple until one of them can be proven right, and challenge for the right to the island.
However, neither side has been proven yet, so they have been stuck in a stalemate, unable to return to their home (The Temple). The MiB has been looking for a loophole to kill Jacob, since if he is killed, then the point can be proven that people can be manipulated into wrongdoings for what they think is for the good of others. The MiB did this by manipulating, and later possessing, Locke into believing that he was one with the island which allowed for others, including Ben and Richard into unknowingly working against Jacob.
Jacob must have know this because he has been working to negate the use of the loophole through his own little manipulations, or just a little push" as he likes to say, of the Losties.
Now, here's where it gets interesting. Jacob, knowing that the MiB's plan will have him killed visits eight of the Losties (Kate, Sawyer, Locke, Jack, Sayid, Hurley, Jin, and Sun), six of them before the 815 crash would have taken place (Kate, Sawyer, Jack, Locke, Jin, and Sun) and two after the Oceanic 6 were rescued (Hurley and Sayid). I think that the interactions that took place before the plane crash were set in the alternate timeline where 815 never crashes, and the visits to Hurley and Sayid take place in the original timeline. This is important, because now Jacob has people unknowingly working for him in both realities. I also think that when Jacob touched all of them, he gave them a link to the other reality. This could explain why they had confused looks of déjà vu in the alt. reality. They remembered something, they just didn't know what. It is going to be up to the Losties in the alternate reality to realize what has happened and find a way back to the island, ! but I think it will have to be the island sometime in the past, because in their reality, the island is at the bottom of the ocean.
Back in the original timeline, Hurley has become acquainted with Jacob, and can now communicate with him, because Hurley can communicate with the dead. This is why he was chosen by Jacob. Jacob told Hurley that Sayid needed to be brought to the Temple to be brought back to life. I'm not exactly sure why, perhaps to be a host body for Jacob, or the original ruler of the island I had mentioned. Or perhaps he is working for the MiB now.
Now you have two separate realities and a group of the same people in both. I think the alternate reality people will be brought together in different ways, and slowly recollect their other reality on the island. The original reality will be busy fending of the MiB while also slowly realizing that there is an alternate version of themselves. This would explain clues like Juliet telling Miles that "It worked", she was like Desmond, and was unstuck, not in time, but in reality. As both groups discover that there are two versions of them, they will also find out that they need to be reunited. Somehow, I'm not sure how yet, they will find a way to recombine the two realities. And like I said before, I think they will recombine sometime in the past, when the island was in the same state in both realities. Another thing… I think it’s very important that Locke's body is still on the island. Perhaps alt reality jack will fix Locke's paralysis, like he hinted in the airport.
Once the two realities are combined, all of the Losties will once again be together alive and well, including Locke. This may cause the MiB to abandon Locke's form and take his own once again as we saw in The Incident. With Locke back to his old self, but with a little more confidence (I still think he has a big part to play for Jacob's plan), the Losties will finally be able to stand together ready to battle for the side of good.
Only together will they be able to rise above and defeat evil. Like Jack said way back in season one, "Live together, die alone." Through this, they will prove that everything else up to that point was "progress" and though they've been through points in which they've destructed and corrupted (as the MiB said), they've progressed past that and have finally come to an ending together. This is detrimental to the MiB since his entire argument was to prove that this wouldn't happen.
I have no idea about how this will all end, or if any of what I said is accurate, and there are still a lot of things on the show that this theory doesn't cover that will most definitely play a major role. However, I can only theorize on things that have been presented to us or at least hinted at. Who knows? I guess we'll find out in the coming weeks.