The movie strongly suggests that Kevin Spacey's ...(Spoiler)
...character is all human.
I watched the movie three times. I'm convinced the movie is all about being Prot a variation in the mind of Robert Porter who survived his attempt to suicide and couldn't get over what he had found in his house. Without this second personality he couldn't connect to the real world anymore. When he decided to let his Prot personality have an end after 5 years he cut his connection to the world.
There are hints in the movie that (mis)lead us to the conclusion he is an alien. But at the movie's end it's obvious these were red herrings.
I haven't read the book. I'm talking about the movie. Some kids like the idea of Prot being an alien. But that would make this movie very bad for me. I like the scene with Jeff Bridges in that house. It's the conclusion of the story. Robert Porter had gone through hell. He IS an alien of a certain kind from that moment on. But he is definetly not from a far planet. He has a split personality. That's what the movie is about.