Christian Shephard was has been used by MIB since his corpse landed on the island via 815. I believe that MIB (who is also the smoke monster) scanned Jack - either with Jack knowing or not - There is so much more to that scene from the pilot where Jack conveniently goes missing during the chase from the monster on the way to the cockpit! After scanning Jack of his memories, very much the same way of Eko, he was able to realise that he could use Christian to lure Jack out into the jungle. And if we remember correctly he tried to kill Jack by running him off a cliff! That is going to be no one else than MIB! I dont know why he tried to kill Jack, but its evident that Jacob and MIB´s intelligence transcend space and time, and maybe in the future Jack is key in bringing about MIB´s demise and he tried to stop that early.
Next we notice that Christian´s coffin is empty, very much the same as Yemi´s missing body - obviously a hint that the same thing has happened, and Yemi has been more or less confirmed as being the smoke monster.
Next we see Christian in the cabin. Its been confirmed by Ilana that ´someone else´had been usung the cabin for a very long time. The first time we hear this figure is the help me scene where I believe MIB is asking John to help him break free of the loop he´s in with Jacob. Then when John goes to the cabin again, Christian is there. When John says he was chosen to be there, Christian is obviously laughing at him on the inside, he is using John. He tells him to move the island - why? because when he leaves Widmore, MIB´s follower, will be there waiting to feed John a story how he is special and needs to be on the island for a war - and probably even kill John before sending him back to the island.
But Ben turns the wheel and is sent off the island - and John is sent skipping through time, until Christian tells him to go off the island and MIB, in the form of Locke, strengthens the plan by telling John himself that he has to die, obviously now desperate for this to work. Also, when Flocke takes Richard and Ben to the drug plane, he suddenly is able to describe how it flew from Nigeria and crashed here. Specific details for a man who only found it and never really talked about Eko´s entire history with it. He knows, because MIB scanned Eko and thats how he knew everything about the plane.
The plan works, John is brought back to the island dead. When Sun and Frank go to the main island they see Christian who tells them to wait for John, so they are now on the same side so to speak. That night, on hydra island, Ilana tells Ceasar something interesting. We dont see it, but its interesting. She says that they found a man in a suit standing in the ocean. A very clever trick by the writers as that is how we are first introduced to Christian/MIB - when Jack sees him he is standing in the ocean in a suit. Its obvious that John is now MIB also.
Flocke then manipulates Ben (which is why i believe MIB wanted Ben to stay, and not turn the wheel, because he has always been part of the plan) by usinghis daughter, into killing jacob.
The only thing im having trouble understanding is why there are two John Lockes. But this could easily be expplained as anything - from time travel to the fact that we still dont really know MIB´s process of taking over the dead, he could just scan the body and make a double - and the reason he takes the bodies is to make sure no one finds them and realises he is a fake. I think its that simple. He just didnt have time to search for Lockes in the cargo, or there were too many people to catch him. He´s desperate at the moment and his time is so close that he´s rushing to finish the plan.
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