A brave exiled from Cochise's stronghold takes Jeffords as prisoner, because he falsely believes he is responsible for an ambush on his exile group. He wants to exchange Jeffords for his daughter, who the brave falsely believes was snatched in the ambush.
Jeffords convinces a reluctant Cochise to re-investigate the case of a father and son held to be traitors to their Apache ways. The son claims the man held to be the hero was the real traitor, costing the lives of ten warriors, and he hopes to avenge and clear his late father's name.
After a Chiricahua brave is scalped on the reservation, Cochise and Jeffords go to Mexico to confront a hacienda owner who pays a bounty for Apache scalps and are caught in the middle of a Coyotero raid.
When Geronimo's braves conduct a foray into Chiricahua land to steal horses, Jeffords must swear in Cochise and a limited number of Chiricahua braves so that they can be legally off the reservation to pursue the renegades and prevent a defection from Cochise.
A hold out group of confederate soldiers come out of Mexico and raid the Chiricahua reservation, which requires Jeffords to go to Washington to ask for help from President Grant to prevent Cochise from breaking the peace.
Jeffords must arrest Cochise for destroying a cavalry supply wagon. Cochise is silent on the reason: to prevent his son, the war leader of the Membres Apaches, from being involved in an ambush on soldiers.
When a rancher becomes deathly ill, his daughter says that to keep the ranch going she can no longer honor her father's word to supply beef to the Chiricahua. Jeffords and Cochise are later suspected of poisoning the rancher.
During a drought Cochise requests the help of an eccentric alcoholic diviner, despite the skepticism of both settlers and braves, while the settlers attempt to divert a stream from the Chiricahua stronghold.
Jeffords and Cochise go to free Chiricahaus imprisoned in land in the middle of Arizona treated as foreign country because of a Mexican War treaty and discover that criminals fraudulently preserve the territory with a fake heir.
When a boy from a criminal family is caught stealing, Jeffords takes custody of him to prevent his imprisonment. But he then farms the boy to Cochise to teach him life lessons, to the mortification of his parents and the settlement folk.
A cavalry unit returning from an ambush mistakes an Apache group waiting for peace talks as a war party and slaughters the group. Cochise is persuaded to talk to Chief Nana in an effort to convince Nana that there is still peace.
Cochise suspects something is amiss when an outlaw matriarch has Jeffords kidnapped to use as a bargaining chip for the life of her son. The son is being held by a Coyotero chief whose life Jeffords once saved .
Jeffords is falsely accused of stealing supplies meant for the Chiricahua reservation, which spurs efforts by Cochise to thwart Jeffords' prosecution, despite Jeffords' insistence on following the judicial process.
Cochise's son Tahzay enters into a competition to be village chief, but his opponent Koteeja plans to cheat and murder him. When Jeffords convinces Cochise of the treachery the two try to thwart the plot.
Mexican emissaries cajole Cochise into returning a valuable golden Aztec idol, taken in an Apache raid, for a Mexican heritage museum. But the idol is stolen by bandits when leaving the Chiricahua stronghold.
A Chiricahua brave acting as an army scout is with an officer when the officer dies after being in an area with reported bubonic plague. The brave is quarantined but escapes and flees to Tucson where fear spreads among the citizens.
Two nuns arrive on a stage from Philadelphia to return a gold statute and run a mission now on Chiricahua land. They must contend with the skepticism of Cochise and a with ruthless fortune hunter who arrived on the same stage.
An army major plots war with the Chiricahua for the dual purpose of avenging his damaged career, for which he blames Cochise, and hiding his complicity with a crooked army contractor to make money from the tribe's supplies.
A brave who deserted the Chiricahuas during war returns to plead for inclusion in the tribe so he can marry. But he is coldly rejected, and draws the murderous hatred of a brave to whom the woman was promised by her father.
A Chinese cook, saved from renegades by Cochise and Jeffords, is bound by Chinese culture to protect Cochise in the future. But he is put in a dilemma when his mining crew, working Chiricahua land, plan Cochise's murder.
An elderly Pinal Apache chief is duped by an ambitious brave to summon Jeffords for peace talks. But it's a ruse by the brave to kill Jeffords and use the murder as a catalyst to inspire a larger portion of the Apache tribes to war.
Cuchillo, a treacherous Chiricahua, convinces young Miguel that he has killed a white man from whom Cuchillo has stolen dynamite, so that Miguel will flee and Cuchillo can hide from Cochise his plan to deliver the dynamite to Geronimo.
Jeffords joins an area posse to pursue a gang leader who sold liquor to Chiricahua braves, hoping to prevent Cochise from rashly pursuing him. But when the posse fails and Jeffords is wounded, Cochise takes over.
When Jeffords is reassigned as Indian agent to the Utes, his replacement proves to be both without the necessary sensibilities and bureaucratic adaptability, so hostilities ensue as the Chiricahuas threaten to break the peace.