When we are first introduced to Jacob and the MIB on the beach they are having a conversation about the ship they see on the horizon. The MIB asks how did they find the island. Jacob responds with you’ll have to ask them when they get here. The MIB then says I don’t have to ask you brought them here. I might be crazy but to me it sort of sounds like he said “I don’t have to ask WE brought them here. But that is neither here nor there until it is all over anyway.
The two then go into the following conversation:
MIB: They come, fight, they destroy, they corrupt, it always ends the same.
Jacob: It only ends once anything that happens before that is just progress.
At the end of this episode after Ben stabs Jacob and he falls to the ground on his knees he say’s twice to the MIB “They’re coming.” The first time it was inaudible. The MIB then seems shocked or aware of the fact that he needed to get moving before something he doesn’t want to happen, happens again.
My suspicion is that the “They” that both Jacob and the MIB are referring to are the same people over and over again. To me this seems like some sort of computer type game where when at the end it just keeps getting reset. The MIB realizes that he has a finite amount of time to “Get off the island” before the reset occurs. If he doesn’t everyone gets thrown back into the game and it starts all over again. Maybe it’s like what Flocke said “But because Jacob chose you. You were trapped on this island before you even got here.” This seems to apply to everyone.
My take on this is if the circle isn’t broken “They” are all destined to keep repeating this game out for eternity. I still believe that Jacob and the MIB are possibly the same entity just insane. The entity is talking to itself giving itself something to hate in the MB. Giving it a noble goal to achieve in Jacob. I believe that something happened in the past that caused the split personality. Something so bad that it has been trying to atone for it for all this time.
Go back and re-watch the episode and look at the MIB’s lips when he says “I don’t have to ask you brought them here. He say’s WE instead of I. 75% of speech is repetitive and that is why when you hear most things the brain just fills in what it expects to hear. This is the Season 5 finale if you weren’t sure.
I don't expect anyone to take me at my word watch it for yourself. Remember when Keamy said what he said about "the island" no one really believed until the next episode when numerous people in the FS were having flashes of the island. A majority of people didn't even believe when they heard it.