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My theory about the motivations is this: The island is special in many ways, but the most important way is that it will survive the end of the world that the Valenzetti equation predicts. Jacob's nemesis doesn't believe people can change, so he just wants to just let the world die, and start things over again with his hand picked group of survivors.
Jacob believes they can change, so he keeps bringing in groups from the outside world, trying to find the ones who can prevent the world from ending.
Jacob's nemesis knows Jacob's plan won't work, but Jacob keeps "trying to prove him wrong", which would be ok, except everytime new people show up, "They come. They fight. They destroy. They corrupt. It always ends the same." Maybe the Nemesis is pissed off because everytime Jacob tries to save the world, Jacob's guys end up accomplishing nothing except killing a bunch of the Nemesis' hand picked survivor group.