Major spoilers in this question, so beware if you have yet to finish the game!
The question isn't so much about what happens to him since the ending is pretty unambiguous in that respect, but rather, what happened to...
his face. Throughout the game you can see the metal clips around his face, which is even a different colour to the skin on his forehead and neck. At the end, after he dies, the mask comes off and you see his real face, with one eye burned and all horrible. Most intriguing is the massive Vault symbol scar, as it looks more like a strip of metal embedded in his skin rather than a scar. You can see his face here.
Is there any reference as to what happened here? Is some past event mentioned or anything? I don't remember hearing anything about it as I was a bit surprised when I found out about it towards the end.