In Gary Paulsen's novel Canyons, 14-year-old protagonist Brennan Cole is the hardworking son of a single mother whom he doesn't see very much due to her own hard work to make a living for them boh in El Paso, Texas. Brennan senses that she considers him to be a burden and, therefore, strives to be independent, earning enough money on his own, working for a gardening service, to be able to provide for himself. Despite trying to avoid his mother, he is one day suckered into joining her, her new boyfriend Bill Halverson, and the church youth group Bill oversees on a camping trip deep in a canyon of El Paso that changes his life.
While in the canyon, Brennan unearths an ancient-looking skull marked by a bullet hole. Fascinated, he brings it home in his backpack. At home, he notices the person must have been about his own age when the person died due to the similar measurements between his own head and the skull. When Brennan starts having disturbing dreams that he is running away from a pursuer, he tells his teacher and mentor, Mr. Homesley, about the skull, who introduces Brennan to a friend who is a coroner.
Upon examination, the coroner determines that the skull belonged to an Indian boy who must have died between 1855 and 1885. Research in the Western Historical Archives leads Brennan to learn about a boy warrior, named Coyote Runs, who was killed by American soldiers in the canyons, just as he was undertaking rituals that if completed would make him a man. Brennan feels possessed by the spirit of Coyote Runs and knows he must take the skull back to the canyon and place it in what is being called "the medicine place," so that the boy's soul can find rest.
The spirit guides Brennan on foot, running, back to the canyon. Though Brennan must escape his mother and the policemen who are waiting for him in the canyon, knowing its where Brennan ran off to, Brennan is able to make it to the medicine place and give Coyote Runs' spirit rest. Through Coyote Runs, Brennan views the world in ways he has never seen before and performs acts of bravery that develop his manhood.