In 1871, two exiled samurai from the Aizu domain, Hikosaburou Soma and Manzou Shiotsu, find themselves hunting for survival in the Bighorn Mountains of Wyoming following their displacement after the Meiji Restoration. While traversing the wilderness, Hikosaburou discovers a dying Native American woman who has just given birth. She is Running Deer, a captive who escaped from white settlers, stealing a bag of gold nuggets to secure freedom for her newborn daughter. After the samurai fend off the bounty hunters sent to retrieve her, their actions are witnessed by a war party led by the Oglala Lakota chief Crazy Horse.

Intrigued by the strangers' formidable unarmed combat techniques—jujitsu, which is unknown in the New World—Crazy Horse invites the two Japanese warriors to his camp. The samurai find unexpected parallels between the Bushido code and the warrior traditions of the Plains Indians, who are fighting a desperate rearguard action to protect their sacred Black Hills and hunting grounds from American expansion, railroad construction, and the systematic slaughter of buffalo. Fully adopting the cause of the Oglala, Hikosaburou and Manzou integrate into the tribe, teaching jujitsu to the warriors while learning the customs of their new home. After proving themselves in battle against their traditional enemies, the Crow, they are formally inducted into the tribe and receive new names: Hikosaburou becomes Sky Hawk, while Manzou becomes Winds Wolf.

The narrative follows their complete assimilation and their pivotal role in the escalating conflict against the United States Army. Notable sequences include witnessing the devastation of buffalo herds by white hunters and participating in the Great Sioux War of 1876. The manga culminates in a detailed depiction of the Battle of the Little Bighorn, where the allied Lakota, Cheyenne, and Arapaho forces annihilate the 7th Cavalry Regiment led by Lieutenant Colonel George Armstrong Custer. Throughout these events, the former samurai fight not only for the survival of their adopted people but also to preserve a way of life they see as spiritually superior to the mechanized, expansionist society of the white settlers who are encroaching from the east.