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In Arizona, after the Civil War, Lt. Col. Owen Thursday and his teenaged daughter Philadelphia stop at a rest station on the road to Fort Apache, where Thursday has just been reassigned as cavalry commander. Also on his way to Fort Apache is young West Pointer Lt. Michael Shannon O'Rourke, who is met by his godfather, the Irish Sgt. Mulcahy, and two other soldier friends. Philadelphia and Michael are immediately attracted to each other, but hide their feelings behind a facade of military decorum. Upon arriving at the fort, the exacting, strict Thursday is briefed about the Apache Indians by Capt. Kirby York and longtime acquaintance Capt. Sam Collingwood, the former commander of Fort Apache. Although Thursday, a demoted Eastern-bred Civil War general who resents his assignment to the remote fort, scoffs at reports of Apache insurrection, York, a seasoned frontier fighter, advises that the Apache threat be taken seriously. Later, Thursday confers privately with Collingwood, a fellow Civil War veteran who, unlike Thursday, has enjoyed few promotions. After discussing Collingwood's upcoming transfer, Thursday talks privately with Michael's father, who is a noncommissioned sergeant at the fort. Thursday learns that Michael, whose professional demeanor has greatly impressed him, received his West Point commission because O'Rourke won the medal of honor during the Civil War. The next day, while Philadelphia, Collingwood's wife Emma and Mrs. O'Rourke turn the barren commander's quarters into a presentable home, Thursday receives word that a general alarm has been issued at neighboring Fort Grant. Despite the alarm, Michael takes Philadelphia riding the next morning, and the couple comes across the bodies of several massacred soldiers. After riding furiously back to Fort Apache with Philadelphia, Michael relates his findings to a worried Thursday. Although appreciative of Michael's detailed report, Thursday forbids the youth to see his daughter again and orders him to lead a small detail to retrieve the corpses. While Michael's detail picks up the slain bodies, Thursday, an avid, if unimaginative strategist, orders a platoon to follow the detail's wagons. As hoped, the wagons are attacked by gun-wielding Apaches, who are then chased off by the platoon. Later, Thursday and York angrily confront Silas Meacham, the local reservation agent, about selling "rotgut whiskey" and firearms to the Apaches. Although the greedy Meacham maintains his innocence, Thursday discovers that the general store's scales have been fixed and finds liquor where Bibles should be. Once back at the fort, York convinces Thursday to allow him and "Johnny Reb" Beaufort, a Spanish-speaking soldier, to approach Cochise, the leader of the rebel Apaches, alone and unarmed. While York and Beaufort ride across the Mexican border to the Apache camp, Philadelphia and her father argue about her future with Michael, who has just proposed to her. Thursday tells Philadelphia that, as the son of a non-commissioned officer, Michael can never marry her. He also informs her that he is sending her back East, where she must remain until she reaches legal age. Later, York and Beaufort interrupt a fort dance to report that, as arranged by York, Cochise is returning to Arizona to talk peace with Thursday and Meacham. Despite York's pleas that his promise to Cochise be honored, Thursday orders that the entire Fort Apache regiment report for battle. The regiment is quickly surrounded by Cochise's superior forces, however, and Thursday is forced to order York to negotiate a peaceful settlement. The proud Cochise, who is accompanied by Geronimo and other Apache leaders, demands that Meacham be ousted as a condition for peace, and threatens to "kill the whites" if this stipulation is not met by dawn. Outraged by Cochise's demands, Thursday decides to attack the Indians and orders his troops to ride into battle in groups of four. When York protests this strategy, which he calls "suicidal," Thursday relieves him of duty and orders that Michael and he man the supply wagons. As predicted by York, Thursday's approach proves disastrous to his troops, and he, too, is shot. After sending Michael to Fort Grant for help, York rescues Thursday, who insists on continuing, despite his wounds. Thursday joins his dug-in regiment and, while fighting alongside O'Rourke and Collingwood, who is unaware that he has just received the teaching commission he has longed desired, is attacked and killed by the Apaches. York and his contingency, the regiment's only survivors, then surrender to Cochise. Years later, after Philadelphia and Michael have married, York, now the highly decorated commander of Fort Apache, defends Thursday's reputation when questioned by reporters about the massacre. After stating that the spirit of Thursday's doomed regiment lives on in every new recruit, York rides off to face Geronimo in battle.