Penumbra overall storyline and a few questions?

[Phil66b]

Between BP and Requiem is so hard to understand, because when the Tuurngait brings you back to the Examination Room at the end of BP, it looks like a moment back in time, but if you throw objects at walls, they just disappear. I'm flip-flopping between if it's an illusion, hallucination, or real? The computer's obviously real.