Nathan Algren is an American hired to instruct the Japanese army in the ways of modern warfare, which finds him learning to respect the samurai and the honorable principles that rule them. Pressed to destroy the samurai's way of life in the name of modernization and open trade, Algren decides to become an ultimate warrior himself and to fight for their right to exist.

A nameless ronin, or samurai with no master, enters a small village in feudal Japan where two rival businessmen are struggling for control of the local gambling trade. Taking the name Sanjuro Kuwabatake, the ronin convinces both silk merchant Tazaemon and sake merchant Tokuemon to hire him as a personal bodyguard, then artfully sets in motion a full-scale gang war between the two ambitious and unscrupulous men.

The background to and depiction of a watershed battle in Japanese history, at Sekigahara in 1600, when Tokugawa Ieyasu's Army of the East defeated the Army of the West of Ishida Mitsunari. The story includes the intrigues and shifting loyalties of the various retainers, family members, and samurai.