The Light transformed into the Smoke Monster
Across the Sea gave us lots of answers. Still it did leave a gap to what happened between (a not so evil) MIB's death and the rise of the evil incarnate, the Smoke Monster.
Here's my short theory on what exactly the Smoke Monster is:
The Smoke Monster is not MIB.
The Smoke is the result of a hybridization between the Light and a Human. Every Human carries something bad/evil inside him (as remarked a lot in the show), while the Light itself represents pure goodness. So the moment MIB came in contact with the Light, the Light lost its "pureness" and transformed into something new: Something corrupted and evil: The white Light (beeing pure goodness) became black Smoke (beeing pure evil).
This hybridization generated pure evil, which is why Fake Mother's purpose was to hide the Light and Jacob's purpose is to keep the Dark (alias the "new" Light) on the island.
It also explains, why the Smoke Monster wants to leave the island: Because he got his personality from him.