Locke and Christian by lostbutimfound

Locke has been the Man in Black (MiB) and Christian's ghost has been an agent for Jacob since day one of them landing on the island.

In the episode, "The Brig" Locke's father says that he woke up gagged in a room and "there was my dead son". Somehow, Locke died before the crash and became MiB as soon as they crashed. Hence the reason why Locke is "special" and has a "special communion with the island". This is also the reason why Locke is the only one not afraid of nor killed by the smoke monster when being "judged" and also the reason why he was miraculously able to walk after being paralyzed for 4 years prior to the crash. John Locke was dead before the crash and the MiB immediately assumed his physical form. Since they crashed, the MiB has been performing a long con on all the survivors and the others in order to regain control of the island permanently without Jacob. he can also assume the physical form of others who have died before coming to the island (i.e. Eko's brother, Yemi who was shot and most likely died long before their small Beechcraft ever crashed on the island).

Christian, on the other hand is really the ghost of Jack's father. We never see or even hear whether or not his casket and body actually made it to the plane. We assume it did, but when Jack opens the casket that he thinks his father's body is in, there is no body to be found. Either it was Locke's casket or it contained no body to begin with. This is why Christian is really the ghost of Christian working as an agent of Jacob to help the survivors of which, one will replace Jacob. Christian is doing this out of guilt and regret of his fatherhood towards Jack and wants to redeem himself by helping him and the rest of the survivors.

There's plenty more I could put to this theory but in order to maintain some brevity I have condensed it.