Yuma is in a town where the people's failure to accept the war's outcome encourages a boy to seek revenge for his father's death by killing General Grant. To dissuade the boy, Yuma relates a tale of his own struggle with the outcome at Appomattox.
Jeremy Hake receives a double blow of bad news---that his mine is worthless, and that his family is in need. Hake commits murder in a robbery attempting to help his family. Hake asks Yuma to surrender him for the reward offered for the murder and give the money to his family.
Yuma stops at a bar where a bounty hunter is holding the wife of the outlaw he hopes to collect on. Seeing Yuma's descriptive resemblance to the outlaw, the bounty hunter decides upon an alternative plan---killing Yuma and passing him off as the outlaw. Will the wife go along with this idea?
Bull Hollingsworth asks Yuma to take his son Seldon to town to get some life experiences in being a man, and to collect a debt from a saloon boss who is not very willing to pay it. That part puts Yuma and Seldon in some danger.
Yuma is shackled by a sheriff to Traskel and forced to flee on foot with him when Traskel knocks out the sheriff and the horses ride off. Traskel believes that his twin brother is in pursuit and wants to kill him.
Yuma's friend Jim Colburn has been found innocent of a murder for which he was to hang. Before the news of his innocence arrived, Colburn escaped from jail with a posse unaware of his innocence in pursuit.
Yuma witnesses as Roy Shandell murders his partner to keep the money from a stage robbery. Yuma nabs Shandell and delivers him to the Socorro jail but Shandell's father uses nitroglycerin to force the son's release.
After his horse is killed by Apaches, Yuma is found by a stagecoach driver. On the stage is Travers, who is blind and tormented by a previous stagecoach encounter with Apaches, in which his wife was killed when they were left by a driver.
John Sims, Yuma's godfather, saves him from an attack by Indians at his campsite. He asks Yuma in turn to help him track renegade Indian Masi and take his scalp, as revenge for the killing of his wife.
Yuma stops to visit Dunsen who arrives in town and commences to randomly shoot townspeople. The townspeople believe Dunsen's war service has driven him mad and want to kill Dunsen but deputy Maggio permits Yuma to talk Dunsen to sanity.
Yuma aids Ulysses Bowman in a gun battle and accompanies him back to his camp where Yuma learns that Ulysses is in the habit of offering a chest with two hundred dollars to any man who will marry his daughter Felicity.
A woman doctor, her sister, and their ailing father have been left behind by townspeople fleeing hostile Indians. A group of Mexican insurgents led by a demagogic Commandante and bent on reclaiming old Spanish Land Grants arrive in town to take advantage of the situation.
George Campbell, who blames Yuma for his brother's death in the war, provokes a gun battle in which Yuma is wounded after being forced to kill Campbell's nephew. Yuma's godfather John Sims then comes to help Yuma escape from Campbell's vengeance.
When a newswoman observes Yuma defending a boy against an adult bully, she decides to promote him as the typical Western hero in a news story, much to the Yuma's displeasure and possibly detrimental to his safety.
Yuma is chosen by an esteemed but unethical itinerant actress to take part in her performance. While Yuma and she dispute wages, they are kidnapped by a man who demands that the actress performs for his traumatized daughter.
Yuma arrives in a town in which an old friend of his father is sheriff. He learns an advance team of marauders, including the man who killed Yuma's father, has arrived. But none of townspeople, including the sheriff, want to defend the town.
Yuma rescues Arthur Sutro, who was staked to an ant hill by Indians. Sutro tells Yuma he is responsible for him now. But Sutro wants to rob Yuma's peacefully reclusive and scholarly friend Portal of an imagined fortune of gold.
Elderly Kiowa Sammy Hart is believed to have kidnapped a boy, who has actually gone to stay with Hart in his last hours. But the boy's father is on the hunt planning to kill Sammy, and Yuma hopes to stop him.
Yuma is forced to kill outlaw Jake Fellows in a gunfight and then learns he has a deaf mute son. Yuma proceeds to help the boy find a home but two of Fellows' associates are on the trail to take the boy to recover loot that they think he held.
An embittered confederate prison camp survivor talks Yuma into a card bet of two weeks servitude on the man's property. When Yuma loses the bet, he learns that service must be under the prison camp conditions the man suffered.
Yuma joins an uneasy voluntary alliance with two other men. They hope to bring back a fugitive bank president from Mexico to testify about a bank failure scheme which may force homesteaders to lose their land. But they will have to evade the Mexican militias in bringing him back.
Three murderous stage robbers hold up the stage Yuma is on, killing the drivers. When they find that a mining executive on the stage was not carrying the payroll with him as they thought, they plan to hold the man's son for ransom until they get it. But a saloon girl offers to take the son's place.
Seeking water, Yuma is forced to side with two brothers who are in a stand off in a feud with their uncle and cousin, who betrayed the brothers' father and brother after a bank robbery, and are now better fortified and supplied.
Because he had been a member of secret group during the war, Yuma is asked by Jefferson Davis' wife to ensure her husband's safety upon his prison release. But one of the members of the group means to kill both Davis and Yuma.
When the posse chasing Ben White and his gang capture White's wife, Yuma is given the task of taking her to a town jail while the posse searches for the outlaw. But the treachery of White's wife places Yuma in a precarious situation.
When Yuma stops to see his old friend Coley Wilks, Yancey Daggett takes Coley hostage. Yuma is then sent to negotiate a deal with Coley's brother, a sheriff, to exchange Coley for Yancey's brother who is scheduled to hang.
A Shoshone chief keeps three prisoners in exchange for three braves held in jail. But Yuma then learns that the braves have already been killed. Since they had killed a white woman, the chief decrees that just two hostages will be executed, and Yuma must decide who.