This is what I got from the movie -
He was an alien, who used that guys body as a "vessel". When the real guy tried to kill himself after his family was murdered, the alien took over his body and got out of the water, which explains why they never found a body.
When he left to go back to k-pax, he left the body and effectively the body was without a brain, a "soul", which would explain the wheel chair thing and not making any movement or speaking, etc.