In the closing days of the American Civil War, Union Army Colonel John Henry Thomas (John Wayne) and company organize one final attack on a small unit of Confederate soldiers, only to be informed after bloodily defeating them that the war had ended three days ago at Appomattox Courthouse in Virginia. Saddened and weary, Thomas leads his men out west towards home with the intention of rounding up and selling wild horses in the Arizona and New Mexico Territories to compensate them for their loyalty, friendship, and war service. Meanwhile, a band of Confederate States Army soldiers led by Colonel James Langdon (Rock Hudson) feel the war has left them with no home, and they prepare to emigrate south to Mexico and serve as reinforcements to Emperor Maximilian, leader of the French intervention invasion of Mexico against the republican government of President Benito Juarez. Langdon torches his plantation home before he departs rather than seeing it fall into the hands of Northern carpetbaggers. At the same time, Thomas and the surviving members of his command meet up with Thomas’ adopted Indian son, Blue Boy (Roman Gabriel), and other members of his tribe from the Oklahoma and Indian Territories. Together they round up a herd of 3,000 horses and take them across the Rio Grande River of the North for sale to Maximilian’s representatives in Durango, Mexico.
Halfway there, Blue Boy discovers tracks indicating that Mexican Comanchero bandits are planning an ambush on the group of Confederate travelers. Blue Boy and Thomas go to warn the emigrating Confederates and Thomas and Langdon meet. Despite their differences, the Americans – Northerners, Southerners, and Cherokee Indians – repel the group of Mexican “bandidos” attacking the Confederate camp, with Thomas’ former Union Army troopers saving the day. Col. Langdon thanks the Northerners by inviting them to celebrate at a “Fourth of July” party – “Southern style”. However, the former soldiers soon relive the war when a fight breaks out. They then split and go their separate ways. Meanwhile, Langdon’s daughter Charlotte and Blue Boy have quickly fallen in love.
When Langdon’s Southern company finally reach their destination in Durango, they find Emperor Maximilian’s forces were chased out days earlier, replaced by ragged Mexican Republican forces of President Benito Juarez, under General Rojas (Antonio Aguilar), who imprison them. Viewing the new foreigners as potential enemies, the Juarista General holds the Southerners hostage, offering to release them in exchange for Thomas’ horses. After Langdon is sent to Thomas’ camp with Rojas’ demands, the reluctant American cowboys agree to pay the ransom to free their brethren. On the way to Durango, Thomas and his men are confronted by French cavalry. A battle erupts with the Americans coming out victorious. Thomas and his men bring the horses to town and pay the ransom for their former enemies. The company of reunited Americans rides out of Durango to return to the U.S.A. Trying to decide what song to listen to as they ride, the group passes over “Dixie” and “Battle Hymn of the Republic” before settling on “Yankee Doodle”. Charlotte and Blue Boy are seen as a couple, while both Thomas and Langdon laugh at how the Confederate Colonel’s daughter has cut Blue Boy’s hair.