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We know Jack's father body was put on the plane (we clearly see the coffin in one of the very first episodes), and we know that someone took the body (probably MIB) from Episode 5, when Jack smashed the coffin into pieces.

Now, since Christian Shepard's body is never found. Where did it go?

Bonus question: Why did the MIB take it in the first place? (we know he can impersonate somebody without literally taking their body)

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2 Answers 2

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It is indeed never answered, but I think given the fact that Yemi (Mr. Eko's brother)'s body was in the Nigerian plane, and then disappeared, shows that MiB probably moved Christians body somewhere else in order to freak out Jack. One good question is why didn't he do that with Locke? Maybe he didn't have the opportunity, maybe he wanted to be discovered at some point, maybe it's just bad writing.

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As far as I am aware this was never answered in the show.

There are a bunch of theories about Christian's body on the LOST wikipedia web page. Notably here is one of the most common theories:

  • During the crash, Christian's body was ejected from the coffin. The ultimate evidence is the sport shoes (possibly Jack´s) we can see hanging in a tree, in the first scene of the pilot. MiB must have found both the body and the coffin. He made Christian's body disappear but kept the coffin knowing that he would be able to drive Jack mad (or, at least, to spread a lot of doubts).

My personal opinion is that the man in black or smoke monster had to take his body to be able to imitate Christians form. How or what the MiB/SM did to assimilate the form from Christian's body nobody knows.

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"[...] smoke monster had to take his body to be able to imitate Christians form." -- Well, in the last season, MIB, imitates Locke without ever being in contact with the dead body. –  Jefffrey Jan 8 at 20:51
    
This could be explained because Jacob was dead at this point. which hindered him from doing so on live individuals before. –  Jared Jan 8 at 20:54
    
Nope, Jacob was not dead when MIB impersonated Locke for the first time (he went to kill Jacob with the Locke "skin"). –  Jefffrey Jan 8 at 20:55
    
You are right, the wiki page mentions "Eventually, and permanently after the death of Jacob, he took the form of John Locke.", but he took johns form to convince Benjamin to kill Jacob. I still in the camp of believing he took the body for whatever reason so he could imitate Christian's form. –  Jared Jan 8 at 21:00
    
After reading more and remembering the later seasons (I should really re-watch it again:) John Locke was indeed dead by the time the MiB took Johns form. Thus it seems the only logical explanation that the MiB can only take forms of dead characters. Whilst doesn't explain what happened to Christian's body, some of the theories pertaining to the MiB deliberately destroying Christian's body as a way to confuse Jack. –  Jared Jan 9 at 1:18

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