As posted in pieces in another thread, here is my theory:
Justin is a warden present in the final battle with Kemmler. Kemmler swaps bodies with Justin, a la Corpsetaker, just before the final blow is struck, killing Justin instead of Kemmler.
Kemmler/Justin then retires as a warden, retrieves the skull and commands the entity to keep his true identity a secret.
Years later, he adopts Harry and orders the spirit to instruct Harry. In order to do this without risking revealing Kemmler's secret, the spirit creates a new personality without the knowledge of Kemmler. This new personality imprints on Harry creating Bob.
Later, Harry inadvertently orders Bob to remember the original personality which almost kills him, to prevent Harry from learning Kemmler's . Harry orders Bob to never remember that personality, so Bob amputates Evil Bob.
My personal theory now: Kemmler is actually hiding in Elaine, without her knowing it.
