This is only a baby theory that I have been rolling around in my head, and it works on the premise that two physical Lockes are on the Island I/E Locke in the box, and Flocke. This is sorta in response to the statement Flocke made to Jacob saying, "Do you have any idea what I had to go through to get here?".
Theory:
1954 Locke comes into Richard's camp, MIB is watching from behind the scenes, He then gets off the Island and posses as; A. Cooper, and impregnates Emily Locke in 1955. John Locke is born in 1956, and is put into the "System" of foster care. He grows up, has a crappy life, and them gets conned by a guy posing as his father.
Anthony Cooper is not his real father because, MIB/Smokey was impersonating him when Emily got pregnant. But cooper didn't know about his so called kid anyway, so Emily Locke told A. Cooper that she needs some money, and that he has a kid in this world somewhere. So he sees a chance to con Locke out of his kidney and does so, then craps on Lockes life after that, then pushes him out of a window, Jacob touches him Yada Yada.
Locke gets to the island and is approached by Smokey (Episode "Walkabout"), and what he really sees is that Smokey is his true father, That would be beautiful to John being that all he really wants in life is to have a Father.
This would also explain why he drew a picture of Smokey as a child.
Something else happened that day he met his "True" father. He was implanted with MIB's essence and was now, unknown to him, fully controllable by MIB. When he turned the Donkey wheel there were two versions of him, (At least I think we will learn this next season). Was it at this point he woke up and was the MIB, but the other version was just John Locke? I think that is what happened Which one was which? One got picked up by Charles Widmore, the other just went back to the island, in the same way that Richard and Jacob are able to come and go.
So "John Locke Son of Blackie" was killed by Ben, and put into a coffin, and brought back to the island, Ilanna now has this version. MIB locke was already on the island setting up for his loophole and waiting for the Ajira flight to land.
That would be a pain in the butt thing to have to do just for a loophole, Hence "Do you know what I had to go through to get here?" this was planned all the way back in 1954.
Theory:
1954 Locke comes into Richard's camp, MIB is watching from behind the scenes, He then gets off the Island and posses as; A. Cooper, and impregnates Emily Locke in 1955. John Locke is born in 1956, and is put into the "System" of foster care. He grows up, has a crappy life, and them gets conned by a guy posing as his father.
Anthony Cooper is not his real father because, MIB/Smokey was impersonating him when Emily got pregnant. But cooper didn't know about his so called kid anyway, so Emily Locke told A. Cooper that she needs some money, and that he has a kid in this world somewhere. So he sees a chance to con Locke out of his kidney and does so, then craps on Lockes life after that, then pushes him out of a window, Jacob touches him Yada Yada.
Locke gets to the island and is approached by Smokey (Episode "Walkabout"), and what he really sees is that Smokey is his true father, That would be beautiful to John being that all he really wants in life is to have a Father.
This would also explain why he drew a picture of Smokey as a child.
Something else happened that day he met his "True" father. He was implanted with MIB's essence and was now, unknown to him, fully controllable by MIB. When he turned the Donkey wheel there were two versions of him, (At least I think we will learn this next season). Was it at this point he woke up and was the MIB, but the other version was just John Locke? I think that is what happened Which one was which? One got picked up by Charles Widmore, the other just went back to the island, in the same way that Richard and Jacob are able to come and go.
So "John Locke Son of Blackie" was killed by Ben, and put into a coffin, and brought back to the island, Ilanna now has this version. MIB locke was already on the island setting up for his loophole and waiting for the Ajira flight to land.
That would be a pain in the butt thing to have to do just for a loophole, Hence "Do you know what I had to go through to get here?" this was planned all the way back in 1954.
