Brennan is a 14-year-old boy living with his single mother in El Paso. He is an introverted, solitary teenager who runs long distances to escape his feelings of isolation and the absence of his father. Though he feels somewhat disconnected from his peers, he works hard at a local landscaping job and shares a close bond with his biology teacher. During a camping trip, he discovers an old human skull, an event that sparks a profound obsession and a mysterious connection.

Coyote Runs is a 14-year-old Apache boy training to become a warrior in the mid-19th century. He is intelligent, sensitive, and deeply spiritual, frequently looking to the spirits of the natural world for guidance and support. His greatest ambition is to participate in a raid to earn a horse, prove his bravery, and gain the respect of his community as a fully fledged adult.

John Homesley is a large, bearded biology teacher and a Vietnam War veteran. He acts as a mentor and father figure to Brennan, sharing his passion for science and music. Homesley is intelligent and remarkably open-minded, taking Brennan's unusual fascination with an ancient skull seriously when others dismiss it as troubling behavior.

Bill Halverson is the new boyfriend of Brennan's mother and the leader of a local youth group. He is a well-meaning, caring man who tries to build a connection with Brennan, though he struggles with discipline and avoiding conflict. His invitation to a camping trip sets the primary events of the story into motion, and his conventional, practical worldview frequently clashes with Brennan's intense personal experiences.

Brennan's mother is a single parent raising her teenage son in El Paso after her husband left the family years prior. She cares deeply for Brennan and desires to build a new, stable life with her boyfriend. She occasionally struggles to understand her son's solitary nature and his sudden, intense fixations, leading to friction in their household.

Magpie is an older Apache man living in Coyote Runs's village. He acts as a supportive friend and mentor to the young boy, lending him a pony so that Coyote Runs can participate in the raiding party and prove his readiness for adulthood.

Sancta is the respected leader of the Apache raiding party that Coyote Runs joins. He holds authority over the group, making tactical decisions such as avoiding a camp of white men and assigning Coyote Runs the specific duty of watching the extra horses.

Stoney Romero is a local man who runs a landscaping business taking care of lawns for wealthy residents in El Paso. He employs Brennan despite the boy's young age, and the two share a practical working relationship as they maintain yards in the scorching Texas heat.

Tibbets is a pathologist friend of Homesley who works at the local morgue. He uses his professional medical expertise to examine the historical skull Brennan finds, providing crucial preliminary details about the age and cause of death of the individual it belonged to.