###Prot is human
- Prot has a human subconscious
- Prot has a human history (e.g. the school book, and the probable trauma)
- Prot remains on earth after July 27th
###Prot is an alien inhabiting a disturbed human's body
- He can see ultraviolet rays (perhaps through the glasses)
- He has an astounding knowledge of astronomy, physics, and advanced psychology (cures patients of serious mental illnesses that are equal to his own if he were human)
- The electrical disturbance on the surveillance when he 'left'
- He managed to disappear and survive unnoticed for almost 5 years since the incident.
- He evaded security and left for 3 days completely unnoticed.
- He left Bess's letter on her bed before she disappeared, confirming some sort of interaction that allowed her to disappear unnoticed on July 27th. (perhaps he told her of a way to breach security)
Regardless, Prot acknowledges his return to consciousness with Jeff Bridges, asking that he take care of him. To me this says that although Prot may be an alien in Robert's body, he may still maintain some of the human subconsciousness.
For these reasons I find the clues are more consistent with the possibility that he is an Alien, than he is not. Funny enough to say, it would be almost more convoluted to argue that he was human.
