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)