This maybe confusing.
So MIB is the Smoke Monster. And we are lead to believe, at this point, that the reason behind this is that Jacob took MIB's body. For reasons unknown and by methods unknown. My theory begins with this... Jacob didn't use some kind of magic, science, or divine intervention to take MIB's body and make him the smoke monster. I don't believe (LoL with LOST I must say "at this point") that electromagnetic energies even had anything to do with it (or at least MIB loosing his body... smokey's creation on the other hand is still up to debate). I believe that Jacob just straight up killed MIB, whether intentional or accidental.
Let me elaborate a little. MIB is evil. We know now that this is the case after the last episode. He does bad things. We also know another bit of information from an episode a little while back. People that die on the Island, that have done bad things, do not get to move on. Anyone see where I am going yet?
Theory in a nut shell... What if MIB did something? Not recently but back years ago. Heck maybe even thousands of years back. We really do not know how long Jacob and him have been on the Island after all. MIB was bad. He murdered someone or multiple someones. Whether his intentions was justified or not he still killed them. Maybe this person or persons had a relationship with Jacob, intimate or otherwise. I'm betting on otherwise, thinking maybe close family... Mother or father. Jacob in turn kills MIB. Maybe not on purpose. Think fist fight because of anger, but he accidentally knocks MIB over a bluff, or he falls and hits his head. Point in case MIB dies, but he cannot move on. He has killed someone on the Island. This would also be the reason for Jacob still being on the Island as a ghost. He killed MIB. He cannot move on either. The rules... all must follow the rules. But I am not talking about Jacob right now I am talking about MIB. So everything is setup now. MIB is a ghost and for arguments sake it is a really long time ago.
So time moves on. People come to the Island and people die. "They come, they fight... yadda yadda yadda" Years pass by. Many years. MIB wonders around on the Island a ghost that no one can see except for Jacob. Giving him lots of time to think. At this point he is not the smoke monster. Forgive me but here is where things get "Lostified."
Old Smokey. Where did he come from??? To be honest I have no idea and no real theory. However I can guess just to move my theory along. Maybe it was made by D.I. to protect them when they very first came to the Island. Smokey does sound man made because of the clicks and ticks it makes when it is flying around killing people. Plus the roar... if that qualifies as a roar and not a screech or howl, that it makes sounds artificial. Maybe D.I. created Smokey for research purposes in the beginning and while running the time traveling scenarios LOST part of it in time. Or possibly the Island will be somehow be related to the Atlanteans, and it will be them that created Smokey for protection purposes. What I am getting at is that Smokey was man made. It was manufacture by "whatever" means as a protection device. It was mindless, soulless, and a perfect vessel for a consciousness to inhabit. And at last the theory comes forth.
I believe that MIB after spending all that time as ghost (No different than Michael a couple of episodes ago) figured out how to inhabit Smokey. Ala a kind of ghost in the machine. Since Smokey had no mind or soul (it was just a machine) MIB simply figured out over the years how to manipulate, use it for his means. Possess it, if that makes what i am saying more clear. He figure out how to do just about everything Smokey was capable of. Shape shifting, scanning memories, etc... and began using Smokey to develop the loop hole that eventually lead to the death of Jacob, and to what MIB hopes will be his freedom. This would also elude to the reasoning about the evil spreading if MIB now Flocke ever left the Island. MIB could potentially take over the world if he so wanted. He cannot be killed because he is already dead. The only way to really stop him will be to destroy the machine that is Smokey.
IMO, this would be a pretty cool way of explaining how MIB became Smokey and maybe even how to stop MIB. Given the origin of Smokey was decent. Again I have no real idea of how Smokey would come to be. I admit that it would be kinda lame if D.I. and time traveling was involved but you never know. It is LOST. My theory is just about how MIB becomes Smokey based on Smokey being technology based and not some supernatural presence. Thank you for your time. Sorry there is no refunds for the amount of time that was taken from you life while reading this. Comments are always welcome.