At a prison camp at Rock Island, Illinois, in the autumn of 1864, Captain Mark Bradford, who became the camp commander after injuries ended his fighting career, offers Confederate prisoners the chance to be paroled. In order to be freed, the prisoners must agree to serve as Union soldiers and protect frontier forts against Indians. The Confederates' leader, Colonel Clay Tucker of Georgia, knows that there will be no further exchanges of prisoners and so considers the offer. After seeing one of his men die in the prison, Clay gets Mark's word that the men will not be asked to fight against their own, then breaks a tie vote among the prisoners in favor of going. Clay is demoted to 2nd lieutenant, and the unit joins the 3rd Cavalry of the Army of the Republic at Fort Thorn, New Mexico. Fort Thorn is commanded by the stern, rebel-hating Major Henry Kenniston, who is frustrated that an injury suffered during his first battle has kept him from the war. At dinner, the major's sister-in-law Elena, a Mexican-American from Monterey, breaks down in tears when Clay relates that he fought at Chancellorsville, where her husband, the major's brother, lost his life. Mark, who fell in love with Elena on the day of her wedding, is surprised to find her there, and she states that Kenniston wrote her that she could reach the fort with an Army supply train, then travel to Monterey with an escorted wagon. She has now been at the fort for six months, and in addition to becoming frustrated with Kenniston's excuse that he cannot spare a wagon escort, she is tired of his over-protective attitude and romantic aspirations. When the Southerners chase some Indians into a mountain pass, Kenniston orders "retreat" sounded, then reprimands Clay in the presence of his men for almost riding into a trap. After the Southerners, obeying Kenniston's orders, execute two men for running whiskey and guns to the Indians, they find out that the men were agents of the Confederate government. Feeling that Kenniston has broken their agreement, Clay joins his disgruntled men in planning to desert. Kenniston then sends the Southern troops to escort a wagon train West, hoping that if they desert, they will do it then, while he is expecting it. Although Kenniston takes Elena's name off the lists of passengers, she hides in the parson's wagon and when Mark spots her hiding, he says nothing. Along the way, Clay learns that Elena has come along, and after he allows her to stay, they grow fond of each other during the trip. The night before the troops plan to bolt for Texas, Ephraim Strong, a Confederate agent who has masqueraded as a merchant, tells Clay of his plan to link Confederate Texas with the Pacific Ocean. Strong hopes to defeat the blockade that is strangling the South and make Californian gold available to the Confederacy. Strong urges Clay not to desert, but to return and gain Kenniston's confidence, as Fort Thorn is the only block between Texas and Tucson, and also bring Elena back, so as not to antagonize Kenniston. After their return, Kenniston still does not trust Clay even though he brought Elena back, and when suspicious wagon tracks are spotted in the vicinity, Clay is not chosen for the patrol. When the son of the feared Kiowa chief Satank is captured, the chief and his warriors approach the fort to demand the boy's return. Kenniston, calling the son a "rebel," orders him shot, whereupon Satank issues a threat and leaves. Meanwhile, Clay has received orders to take his troops to rendezvous with a wagon train and proceed with it to California. Clay takes over command of the patrol from Mark, who had come to regard him as a friend, but when he learns that the fort is surrounded by Satank and his braves, Clay and his men decide to go back, as they know that women and children will die if they desert. During the fight with the Indians, Mark is wounded, and Clay rescues him when an Indian tries to kill him. After fighting has temporarily ceased for the night, Clay apologizes to Elena, who is helping to nurse the wounded, for bringing her back, and she sadly relates that before he died, Mark confessed he loved her. A note attached to a flaming arrow arrives with a message that the Indians demand the lives of the officers in revenge for the murder of Satank's son, but that they will spare the others. Kenniston then decides to go alone to his death and turns over command to Clay, who is now respectful of Kenniston's integrity. When he leaves the fort and the gates close, Kenniston issues an agonizing scream, and his body is recovered the following day after the Indians leave. A rider then arrives with the news that General Sherman has completed his march to the sea and that Savannah is surrounded, leaving the Confederacy cut in half. As the Union soldiers whoop at the news and sing "The Battle Hymn of the Republic," the rebels proudly sing "Dixie." With the news that the war will soon be over, Elena comforts Clay, who despairs that there is now nothing left to go home to. She asks for help to rebuild her home at the fort, and in Spanish, tells him it will all seem better tomorrow.