Penumbra overall storyline and a few questions?

[Ssschah]

So when the hive found out he had betrayed them and he sent that email and he was knocked out, was he killed? Or was he just unconscious and they put "requiem" into his mind so he could supposedly make the right choice again which basically meant if he went with Red in the incinerator then the email was never sent or if he went home on the boat then it was? So if he gets on the boat(the good ending) is it in real life in real time or in his mind?