Whether some people like it or not, the producers did answer most of the questions, in a way: almost everything happening on the island was Jacob's work. He manipulated everything his way in order to achieve his goals. Ultimately, this meant killing his brother. How long was he pulling the string for this to happen, we will never know. But he fooled the MiB and in the end counted on Jack to do the finally deed, which he did. If you look at it is this way, you'll understand most of the misteries and you'll see how the whole plot resolves itself quite beautifully.

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