I am the Kat that Walks By Itself

He arrives on Gallifrey, and comes to the conclusion that it's the Time Lords who set him up and had put him in the confession disk in the first place. They have a long history in manipulating the Doctor, so perhaps the rooms were set up with the clues in the first place? Then he figures out just enough to repeat the cycle. It's basically an eternal torture chamber, which is why I can't figure out why this ep is the "Heaven" one and not the "Hell" one.

As far as the stars, if the Time Lords created the entire setting, it would be very easy for them to create a fake view of the stars that would update and reflect the passage of time. The Doctor realizing how much time had passed would be an important aspect of the "torture" part.