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It's been subject to various speculation, but I'll break down the theories: 1. Rapture was one step away from being Fontaine's, and he couldn't bear living to see his creation being taken over - he chooses to die, because he is a man, and as a "slave," Jack has no choice but to obey Ryan's wishes. 2. He knew Jack was his son, which is why he didn't fight him, I think it was an attempt to be a father to Jack, to show him that he was being controlled. He apparently wanted to die, seeing that his vita-chamber is off. 3. Because he knew Jack was his son, he believed he would be able to force-alter Jack's programming through telling Jack to kill him. He staked all on idealism and lost.