Dealing with nuclear testing and its long-lasting deadly effects, the story portrays Boy, a young widower living in the desert on a nuclear testing site. Living as a hermit, he waits for the end of the world, carving Kachina dolls that he believes have magical powers. While travelling on a "second" honeymoon across the Arizona desert, the car of a Hollywood jet-set couple breaks down. They are rescued by Boy, who holds them prisoner, because he desires the woman, and wants to create a better world with her.
Only 80% of the film was shot when River Phoenix died. For the 2012 release, director George Sluizer filled in the remaining scenes by narrating the script himself.