I'm currently watching Season 1 again, and have found MANY eerie signs that point to this theory: JOHN LOCKE HAS ALWAYS BEEN THE MAN IN BLACK. The first time we see Locke alone (either the 1st or second episode), he's sitting with his back to the ocean, and a dark ominous cloud is coming inland.
Lock also explains backgammon to Walt, and states that it's the oldest game in the world. One side light, and one side dark.
Locke tells Walt a secret which we never find out. We are led to believe that he tells Walt about the wheel chair, but Walt only tells Michael that "a miracle happened."
The episode before we find out about Locke's wheelchair ends with one of Hurley's songs being cut off by creepy music, and a close-up of Locke staring at Michael, Walt and Vincent.
Later in the series, we see that Ben, truest believer in the island and all of its power, is in awe of Locke after finding out that he was cured of his paralysis. Richard Alpert is also in awe when Locke comes back from the dead. It's like the writers have been telling us all along that the island is very powerful, but possibly not THAT powerful.
You would think that this theory would mean that the smoke monster is not the Man In Black. But quite the contrary. What if the Smoke Monster is just another form that both Jacob AND the Man In Black could take. Either that, or the Smoke Monster is Jacob, and what Jacob giveth, Jacob taketh.
Thoughts?