My theory is short and simple. Jack and MIB(Locke) have a struggle/fight which causes the island to sink, killing everyone on the island, including the smoke monster in the process. The impact the island being sunk under destroys the light in the cave which is probably the electromagnetic energy. Destroying this energy will erase everything that has every happend on the island, including oceanic 815 crashing AND Mib and Jacob being born on the island.
This is the main reason why haven't seen Mib or Jacob in the alternate universe, b/c they were born centuries before the 2004 timeline, and thus would be dead by now. Jacob never became ageless and is obviously dead by 2004. This is the reason why everyone who died in oceanic 815 is alive in the alternate world. Everything that happend on the island is erased due to the light in the cave being destroyed as a result of the island being sunk.
There is one kicker thought, which I still don't know, why is Desmond gathering all the oceanic 815ers together in the alternate world? I can't quite put my finger on that one.
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