Canyons is a book about two boys. One boy is named Coyote Runs (age 14) and the other boy is Brennan Cole (age 15).The story starts with Brennan making a short narrative about his life and switches back and forth from Brennan and Coyote Runs.
Later in the story, the switching ends when Coyote Runs gets shot in the head during his first raid that would, if successful, make him a man among his Apache tribe. However, he is shot by American soldiers and dies instantly.
Nearly two hundred years later, Brennan finds his skull with a bullet hole in its forehead, and becomes obsessed with it. From that point on in the novel, a mystical link connects Brennan's mind with Coyote Runs' spirit. After talking to his old biology teacher, he runs sixty miles in a day and a night to return the skull to the top of a canyon - a place Coyote Runs calls his“medicine place." After a grueling run and a chase by Brennan's search party, he gets Coyote Runs' skull back to the medicine place, ending the bond and the novel.