I'm not going to create some long crazy theory, so here's a simpler and possibly strongly grammatically incorrect, so pardon me..
Hundreds of years ago, a young explorer and his wife, a fellow explorer discovers a very odd island, like no other along with another group of explorers. He is drawn to this Island, but the strangest part of his short journey is, he gets sick and dies. His wife takes his death harsh, she goes mad and dies right next to her husbands body.
They are not found until about a century later, where the island yet again gets discovered; this time on purpose. A man named Alvar Hanso develops the Hanso Foundation, in order to use an Island to develop different experiments; also create a better well-being and a better tomorrow. However; they have no idea that the Island was going to do experiments on them.
After a while, the Hanso Foundation was doing good. That's until Dharma came along. Dharma Initiative had the upper hand. They had a big plan for the Island. They were going to develop stations on the Island, in which various experiments will be executed. Eventually, the two came to an agreement and they become one corporations. A couple years later, Dharma accidentally caused an extreme electromagnetic shield, and it causes the Island to slip in different time zones. The Swan needed to be built, in order to keep this massive amount of energy controlled. The button failed to be pressed, and BAM. Oceanic 815 crashes. Sends the entire Island into 1996. They've been playing on this timeline the entire time (besides there recent flashes of course). This is why Rose is cured from her cancer; why Locke can walked.
Where does MIB and Jacob come in? MIB is simply the evil that was meant to tempt Jacob. Jacob is the original's explorers replacement. Until now, he didn't need a replacement. He had it all under control. Until Hanso came along, and caused all this mess. This is why the MIB wants to get off the Island. To release the evil and time glitch into the world. MIB is simply the snake in the classic Adam & Eve tale. He was meant to be a distraction to the original explorer, as well as Jacob, and even the possible candidates now. I shouldn't call him a "he", it is a smoke monster, of pure evil.
Jack fixes the time glitch in the Finale, and eventually kills MIB. None of this happens; and Jack basically saves the world. He still needs to be the new Jacob, to protect something like this from ever happening again (due to the Island's mass potential of unexplainable phenomenons). Also, Desmond is using the two realities to merge in order to fuse two totally different timnelines, to become one, and potentially solving this time glitch; after all, it was his fault. Sorry if I didn't mention a certain mystery, which I know I haven't mentioned a ton but I don't have all the time in the world. You guys can make up whatever I haven't mentioned, thanks.
PS - If you're curious about the title, look up the lyrics, I thought it fit quite magnificently. :D