[SPOILERS] I think I may have figured this out
One thing that bothered me when I watched this movie was "what actually happened to Bess?"
This is my theory:
Prot is an alien. Robert Porter is his vessel. There is dialogue between Jeff Bridges' character and Prot where Jeff Bridges asks "Why do you appear human?". Prot responds saying that it is the most ideal shape for Earth, similarly if he was on K-PAX he would appear K-PAXian. Also, Prot sees in UV due to there being very low light on K-PAX.
When Prot goes back to K-PAX when the surveillance cameras go blank, his body (or vessel) is left behind and found under the bed. Now, with Bess it is never explicitly understood or explained what happens to her. To the viewer, she is no longer in her room... Or is she?
Could it be that Bess is actually under the bed also? Let us think back to Prot declaring his need to appear human to cope best with Earth, and also think back to Prot seeing in UV. Bess, in human form, would not be able to live on K-PAX. Her human body probably is not best suited for K-PAX nor is her eyesight. For her to survive on K-PAX, surely she would need to appear K-PAXian? Would it be too much of a leap of the imagination that Prot actually took Bess back to K-PAX but just simply took her conscience? Prot was interested in what everyone had to say about why they should be taken to K-PAX, understanding their character rather than their physical attributes.
I thought I would just share this with you all and see what you think?