I jokingly told my friend coming out of the film that it's a giant analogy about the government being behind 9/11. But yeah it just seems too ridiculous to be he was crazy this whole time. I mean the only character that I found that could support that whole story was Max von Sydow's character, since he seemed to be analyzing him the whole time and knowing more than he should. I mean the patient writing "run" in his booklet makes no sense, whether she's crazy or not.

But my guess is that the hospital found out that he was investigating them, lured him in and tried to get rid of him.