Okay people this is my first blog on lostpedia.... Even though I've been on it over a year... Here goes...
Given that the series is now finished and we are stuck wanting more answers, we must cling to the idea that the writers had more planned that just didnt get panned out in the end, so we come up with ridiculous theories, use a line or two as evidence and wait for the rest of the community to either praise or reject it.... I have this about right yes?
Anyway enough stalling. This theory is based mostly on the episode "across the sea", but calls on other episodes as reference points. I always had trouble believing throwing an unconscious man down a cave of light would turn him into a pillar of black smoke, even by lost's standards. After watching the episode, and the rest of the series, I believe that smokie existed prior to the events of this episode. I believe that it was Smokey that appeared to MiB as a teenager in the form of Claudia... the original long con. Mother had the power to command the monster, as evidenced by the destruction of the village in such a short time.
The monster knew that MiB would be a bigger threat as protector than Jacob, since Jacob lacked the ability to lie and was... well nothing more than a little bitch at that age. That was why smokie appeared to MiB.
When Jacob threw his brother into the source it killed him, though unintentionally. The Monster now had the ability to appear as Jacob's brother, and to torture Jacob indefinately. He used Jacob's dead brothers image, quoted Mother in an attempt to prove to be MiB, all to spur Jacob in matters such as the morality of man, which was yet another long con (the rules stated that the monster couldnt leave the island unless the protector and his/her candidates are dead), if Jacob hadn't fallen for it he never would have agreed to the MiB's challenge to prove man's ability to change.
Smokie made comments about having a crazy mother because it likes to pretend it is man, it enjoys feeling the dirt on its feet, it considers itself a "who", not a "what". It tried to be John Locke when lowering Desmond into the source but failed.... It tried to be Yemi to manipulate Eko in a moment of weakness. It acted like MiB because it gave him a false sense of character. The best lies are told with a grain of truth, so in order to manipulate claire, he used the memories of the MiB's "crazy mother" to make his point.