Some unanswered questions.

[Jinix]

Most of the story is Daniel having flashbacks to what happened when he was there the first time and hallucinations based on his own guilt and fear.
I must admit I don't relate to his character - in fact I'll go as far as to say I don't like him.
My ending was to let Alexander go to 'heaven' or wherever he went and let Daniel pay for his sins... and as for the 'head' guy, I kept thinking of a vegetarian with a goatee that drives an old volkswagon bus and I'm not quite sure why he is in the game.
I think the story and visuals are straight out of a crazy man's head and are imaginary hallucinations brought on by his guilt and fear.