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.