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John Locke has been possesed by Samuel ( otherman ) and is still alive, I agree, this chess game seems to be a loop but I believe it is only like one of many alternative timelines being played out to prove that human beings can visit and use the islands powers without abusing them. John, Jacob and the Nemisis will join forces to fight a third element in season 6 is my guess, and the end result will be a harmony with the island and her chosen inhabitants, proving otherman wrong..and thereby he no longer wants him dead and appreciates the lesson from Jacob. Otherman's hatred of Jacob is his desire to remain on the island by himself, no longer trusting humanity. He hates that Jacob still has faith in civilization and desires interaction with what Samuel sees is a waste of time and a foolish attempt to prove him wrong.