While the Civil War rages on between the Union and the Confederacy, three men – a quiet loner, a ruthless hitman, and a Mexican bandit – comb the American Southwest in search of a strongbox containing $200,000 in stolen gold.

There's a single piece of land around Flagstone with water on it, and rail baron Morton (Gabriele Ferzetti) aims to have it, knowing the new railroad will have to stop there. He sends his henchman Frank (Henry Fonda) to scare the land's owner, McBain (Frank Wolff), but Frank kills him instead and pins it on a known bandit, Cheyenne (Jason Robards). Meanwhile, a mysterious gunslinger with a score to settle (Charles Bronson) and McBain's new wife, Jill (Claudia Cardinale), arrive in town.

In the Texas border town of Frontera, Sheriff Sam Deeds (Chris Cooper) digs up the past when he finds an old skull in the desert. As he traces the murder of Sheriff Charlie Wade (Kris Kristofferson) 40 years earlier, Deeds' investigation points toward his late father, the much-loved Deputy Buddy Deeds. Ignoring warnings not to delve any deeper, Sam rekindles a romance with his high school sweetheart while bringing up old tensions in the town and exposing secrets long put to rest.