Well congrats on beating the game! So what happens in this game? I guess that's the final puzzle.
So I'm still planning on expanding the endings, which will help answer some more questions, and changing some of the journal entries to hint at some other stuff. So I don't really want to explain things too much at this point. But I will say: Yes, you are the apprentice. And: No, you never revive Charles. The 'escape' ending is still missing from the game, so that's why the whole game feels so grim and hopeless at the moment. You're damned no matter what you choose to do right now.
Thanks so much for sticking with this game! I'm going to give you a special thanks in the credits. =)