Jacob, MIB, future Dharma and the End of the World by Blockparty

Perhaps this has been stated before, but how's this for an idea...

Jacob is really smart, and from the future. Utilizing the sweet time travel properties of the Island, he's travelled back in time (along with his assistant, MIB) as part of a Dharma experiment to alter the timeline and prevent some future calamity. He's been doing this for a long time now, trying over and over again to get the all of the variables to line up just right in a perpetual loop.

"It only ends once. Anything that happens before that is just progress."

So far, he hasn't managed to get it right. But he's close. Perhaps what we're seeing is the final iteration of this loop, the one where Jacob finally manages to put the pieces in place to change the course of history (and by extension, the future) in such a way that the end of days is finally avoided.

MIB is part of this team of future Dharma scientists tasked with changing the world, but he's jaded. He's given up. He's seen this story play out too many times already and is convinced there's no hope. Instead, he's forced into reliving the same life over and over. Now he's become obsessed with ending it, at whatever cost. The only way he knows how is to kill Jacob, ending the cycle once and for all.

Oh yeah, and Alpert is part of this too. He's in on the plan ("I'm like this because of Jacob"). And perhaps the newbies (Bram, Illana & Co.) are part of this too. Sent as reinforcements on a different flight that was passing through the right coordinates at the right time to get on the island.

What we already know is that Jacob is some sort of time traveller, able to show up at very important moments in key people's lives, nudging them ever so slightly in a certain direction of his choosing. Perhaps this theory explains why.