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I believe that Jacob and MIB are both Aaron, Clare's baby.
Aaron is suppose to be raised by Clare, but is being raised by Kate.
Because of Aaron being raised by Kate, MIB (Man in Black) is winning the battle.
Since MIB is can turn into people, he has appeared throughout the series. In the episode "There is no place like home", Kate was awaken by a phone call, it was whispers, but replayed backgrounds, it said " take him back to the island " and such. Couple seconds later, she heard noises in Aaron's room, it turned out to be Clare, and she screams at Kate telling her "Don't you dare bring him back, Kate."
MIB transformed into Clare, to tell Kate to continue raising him. Why though? So he can win the war.
This could somewhat explain the White(good) and Black(bad)idea because Kate is dangerous and could lead Aaron to obtain her personality like the MIB has.
Of course there is flaws to this theory like "Why are there two separate people than?", well i haven't been able to think of that.
What do you guys think?