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I think the war is between Jacob and Bad Guys(like Charlis Widmor and DI or the bad guys or bad team as Jacob' guy said to Miles) who they want take over the island to control the power then take over the world that's what Charlis want, So Man in Black is just a Guard no more ,this guard want to quit from his job but his friend Jacob won't that happen. If any one have evidences support to that: thanks