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Pretty out there theory, probably isn't right, but I just thought it'd be worth mentioning.
Throughout the conversations we hear between Jacob and his enemy at the beginning and the end of the season finale, they never say they hate each other or anything. Actually, besides the 'I want to kill you' part, they act like good friends, or at least friendly acquaintances. If you were alive for centuries, wouldn't you want to eventually die? Could it be that Jacob and his enemy are stuck in a timeline, constantly timetraveling, or something else that makes them not age? Maybe they both want to die, better dead than stuck in the same body for hundreds of years, protecting an island. Perhaps when his enemy says "Do you know how much I want to kill you now?" isnt out of hate, but of love? Sounds cheesy I know, but Jacob doesn't at all seem opposed to the thought. To expand on a possible plotline, perhaps even though they want to die, they can't kill each other because 'the island wont let them'. They're not supposed to die, even though they want to. But then his enemy/Flocke finds a loophole. Jacob tries not to be tempted when Ben and FLocke come, but once Ben yells at him, he says "What about you?" I mean, what type of person would say that to a man with a knife if they wanted to live?
I know the theory's probably not true, but i just wanted to make it clear that Jacob and his enemy (or friend..) never say that they hate each other or anything.