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I've been thinking about the volcano on the Island, mentioned by Olivia in "The Man Behind the Curtain," and its possible connection with the Man in Black/The Smoke Monster. MIB mentions in "Ab Aeterno" that he lost his body (or if you take his words as exactly true) Jacob stole it. What if the volcano erupting in the distant past was what caused the MIB to lose his body, and his humanity? The volcano being the MIB's "kryptonite" if you will makes sense because ash seems to have a negative effect on him, effectively repulsing him. And what if after he was burned by the volcano, Jacob appeared to him, and offered to revive him, in exchange for becoming the security system for the Island. He gave him powers (by touching him perhaps?) such as the ability to shapeshift between dead bodies and a big cloud of smoke (which would also tie into being burned by a volcano), but he wasn't able to inhabit his own body anymore and was stuck on the Island. And perhaps after centuries of being the security system for the Island, the MIB is tired of his role, and starts turning "bad." He begins to plot to kill Jacob so he can leave the Island, but Jacob doesn't want to let him leave because he knows the powers he bestowed on the MIB would be catastrophic if they spread to the real world. The fact that the MIB might have been on the same side as Jacob and the Island is supported by the fact that there is a chamber beneath the Temple where he seemingly resides, and that Rousseau called him a security system, and Robert called him a security system that guarded the Temple.
What do you think?