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I was under the impression that Jacob is "the good guy". But after watching more closely the end of season 5 and these two episodes in season 6, I think this could be wrong. Maybe the MIB is not so bad after all. He says to Ben when he's in the form of Locke that he wants to go home. Does this imply that he is being held hostage there somehow? maybe the MIB is just a protector of the island and Jacob is the evil-doer. After all, Jacob is the one bringing people to the island.