After murdering John Locke, Ben carefully posed him to make the death appear to be a hanging suicide, cleaning the room of any fingerprints or forensic evidence. As he left the room he said, solemnly "I'll miss you, John." ("The Life and Death of Jeremy Bentham")
Jack first learned of John's death from a newspaper article on a flight home from Singapore. The news devastated him, and he spent several days trying to call Kate to go to the funeral with him. ("Through the Looking Glass, Part 1") When John was later laid out for a viewing at a funeral home, in the name Jeremy Bentham, Jack was the only person to attend. ("Through the Looking Glass, Part 2") Later that night, Jack broke into the funeral home to look at John's body, and was startled by Ben who was also in the room. As Jack left Locke's coffin, Ben mentioned that if Jack wanted to return to the Island he would need everyone to come too, including John's corpse. ("There's No Place Like Home, Part 3").
Later, in a motel room, when asked by Jack if John was actually dead inside the coffin, Ben did not answer. Ben kept John's coffin and body at Simon’s Butcher Shop under Jill's care. ("The Lie") Jack later turned up to take the body, putting a pair of his father's shoes on John. He checked the coffin on Flight 316 claiming he was a friend of the deceased. The coffin and body were on board the plane when it crashed back upon the Island. ("316")