Silver has been found on comanche territory and the government accomplished a peaceful agreement with the indians. When James 'Jim' Bowie comes into the scene he finds the white settlers living near by planning to attack the indians although they know about that agreement and the beautiful Katie seems to play a leading role in this intrigue.
William Shatner plays two roles: cowboy Johnny Moon and his ruthless Indian twin brother, Notah. Notah likes peyote and gets the crazy idea that he's the Comanche messiah sent to lead the Comanche nation against the white man but more specifically the dusty desert town of Rio Hondo. Moon, estranged from his brother, decides to stop Notah either by words or by bullets.
Loner Cody trades with the Comanches to get a white girl released. He is joined on his way back to the girl's husband by an outlaw and his sidekicks. It turns out there is a large reward for the return of the girl, and with the Indians on the warpath and the outlaw being an old enemy of Cody's, things are set for several showdowns.