Season 3 picks up six months after the events of Season 2 and follows Lt. Joe Leaphorn and Jim Chee as they investigate the disappearance of two boys, with only an abandoned bicycle and blood-stained patch of ground left in their wake. Meanwhile, Bernadette Manuelito attempts to settle into her new life 500 miles from home with the Border Patrol, but stumbles across a conspiracy involving human and drug smuggling with far-reaching implications.

In Season 2, Lt. Joe Leaphorn reunites with Jim Chee, his former deputy turned private eye when their separate cases bring them together in pursuit of the same suspect. They find themselves in the high desert of Navajo Country chasing a killer who's turned his sights on them to protect a secret that rips open old wounds and challenges Leaphorn's moral and professional code. With the help of Sgt. Manuelito and Valencia County Sheriff Gordo Sena, Leaphorn and Chee must thwart their would-be assassin and restore balance not only to their own lives but to the reservation that depends on them.