Board Thread:Questions and Answers/@comment-2037710-20130826060145/@comment-4631119-20130830002935

First, he is not bound by the NerveGear rules for player: he's able to log out, and thus we can assume that his head will remain safe no matter how often he dies in game.

Second, in the very end of the anime he appears as afterimage, or a resonance his consciousness, which currently living at the very core of "The Seed". That's why he can appear as a entity in-game. Technically, he's dead on real life, but he still ive eternally in-game, until the time people leaving VRMMO.