Another crappy theory from me! by Jabedoben

MIB is trapped on this island a long long time ago. Jacob is there to ensure that the MIB is never released. MIB has a physical form that can inhabit bodies of the dead. The black smoke is not MIB himself, but a manifestation of him that can travel on the island, impersonate the dead in order to manipulate the living, and kill those not brought to the island by Jacob's "touch".

Jacob brings people, through his touch, to the island again and again over the path of time. He brings Dharma here sometime before 1977. Dharma's goal is not to own the island, but to study its unique properties in order to better mankind. MIBs physical form is eventually trapped inside the cabin built by Horace, perhaps by a joint effort between Dharma and "The Others". MIB can still impersonate the dead from inside the cabin using the monster, but can not inhabit, infect" and control them.

The incident in 1977 involving Dharma and the "pocket of energy" released a force powerful enough to destroy the island. Dharma finds a technology that would keep the energy contained. The Swan, using this technology, was built on top of the pocket of energy. The button needs to be pushed every 108 minutes in order to keep The Swan functional and the energy at bay. Each time the button is pressed, a small amount of the energy is released, counting down to the eventual dissipation of the destructive force.

MIB eventually uses his smokey power to mold Ben from a young boy into the man who would kill Jacob. MIB, impersonating Jacob from inside the cabin, convinces an older Ben, now considered to be the leader of Jacob's people, to instigate the destruction of Dharma. Ben then goes on throughout his life believing he is the leader of Jacob's people, all the while being manipulated by MIB.

In 2004, Desmond fails to hit the button in time, causing flight 815 to crash on the island. The button is then pushed by Desmond, keeping the energy contained.

When the fail safe is turned later by Desmond, the island is not destroyed due to the long term dissipation of the energy.

MIB uses his manifestation of Christian to coerce Claire into breaking the ash circle around the cabin, releasing the corporeal form of MIB himself. All he needs now to return himself to full power is to find a body to inhabit. Once the ash circle is broken, he inhabits the body of John Locke and unleashes his final plan to make Ben kill Jacob. Once Jacob is dead, MIB begins to build an army of "undead", or "infected", to fight the forces of Jacob inside The Temple, and release himself from the imprisonment of the island, enabling him to "go home".

There is a curve somewhere in MIBs "loophole". Jacob, instead of being killed, sacrifices himself.

Something eventually leads to flight 815 never crashing and the off island story line we are witnessing now.