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Is seems as though Jacob is looking for a candidate to replace MIB as the Smoke Monster. That explains why MIB feels he is imprisoned. Not just on the island, but as captive as the island's protector in Smoke Monster form. Once a candidate replaces MIB, he will probably die and he knows this. The only way that he can survive is if he kills all the candidates first. But he can only do that after Jacob is dead. Now that Jacob is gone, MIB may be restored to a human form only and "return home".