At the West Point Military Academy in 1854, the villain Cadet Carl Rader (Van Heflin), a disciple of the fanatic abolitionist John Brown, is dishonorably discharged for spreading anti-slavery pamphlets. His classmates Jeb Stuart (Flynn) and George Custer (Ronald Reagan) become second lieutenants and are posted to Fort Leavenworth, Kansas Territory, the most dangerous duty in the army—an assignment they relish. On the way to Kansas, Custer and Stuart meet Cyrus K. Holliday, in charge of building the railroad to Santa Fe, New Mexico, and his daughter Kit (de Havilland), with whom both officers fall in love.
The Kansas Territory is bloodstained and war-torn, a victim of John Brown's relentless crusade against slavery. Meanwhile, Rader has enlisted as a mercenary in Brown's army, which has been terrorizing the countryside with bloody raids. During Brown's attack on a freight wagon under the protection of the U.S. Army, Stuart and Custer capture Brown's injured son Jason, and before dying, the troubled boy informs them about his father's hideout at Shubel Morgan's ranch in Palmyra. In disguise, Stuart rides into Palmyra, the center of the Underground Railroad, but is recognized by Rader, who takes him at gunpoint to Brown (Raymond Massey). While trying to escape, Stuart is trapped in a burning barn but is saved as Custer leads the cavalry to the rescue and drives Brown into seclusion.
Believing that Brown's force has been broken, Stuart and Custer are sent back to Washington, D.C., where Stuart proposes to Kit. However, far from being defeated, Brown is planning to ignite war by raiding the arsenal at Harper's Ferry, Virginia. When Brown refuses to pay Rader for his services, Rader rides to Washington to alert Stuart of Brown's plans, and the troops arrive just in time to crush the rebellion and hang Brown.