Two Jesuit priests travel to seventeenth century Japan which has, under the Tokugawa shogunate, banned Catholicism and almost all foreign contact.

Down-on-his-luck veteran Tsugumo Hanshirō enters the courtyard of the prosperous House of Iyi. Unemployed, and with no family, he hopes to find a place to commit seppuku—and a worthy second to deliver the coup de grâce in his suicide ritual. The senior counselor for the Iyi clan questions the ronin’s resolve and integrity, suspecting Hanshirō of seeking charity rather than an honorable end. What follows is a pair of interlocking stories which lay bare the difference between honor and respect, and promises to examine the legendary foundations of the Samurai code.

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.

In 1701, Lord Takuminokami Asano has a feud with Lord Kira and he tries to kill Kira in the corridors of the Shogun's palace. The Shogun sentences Lord Asano to commit suppuku and deprives the palace and lands from his clan, but does not punish Lord Kira. Lord Asano's vassals leave the land and his samurais become ronin and want to seek revenge against the dishonor of their Lord. But their leader Kuranosuke Oishi asks the Shogun to restore the Asano clan with his brother Daigaku Asano. One year later, the Shogun refuses his request and Oishi and forty-six ronin revenge their Lord.

In Edo Japan, a kabuki actor seeks revenge against the three men who drove his parents to their deaths years ago.

A young boy named Jiro finds his mother and sister murdered in his home. Falsely accused of the crime, he flees from his village and meets a priest named Tenkai, who has him kill a rogue ninja named Tarouza. After fulfilling that task, Jiro undergoes training to become a master assassin. Many years later, Jiro finds out that he was an orphan and his real father was Tarouza, who had worked for Tenkai until he aborted his mission when he fell in love with an Ainu woman. The young ninja discovers that the Shogunate was to retrieve the lost treasure of Captain Kidd and use it to once again isolate Japan from the rest of the world. Using the clues that Tarouza had kept secret, Jiro - along with the female ninja Oyuki and a slave named Sam - travels to Russia and America to search for the treasure in hopes of using it to extract revenge from Tenkai.

The film depicts carnivalesque atmosphere summed up by the cry "Ei ja nai ka" ("Why not?") in Japan in 1867 and 1868 in the days leading to the Meiji Restoration. It examines the effects of the political and social upheaval of the time, and culminates in a revelrous march on the Tokyo Imperial Palace, which turns into a massacre. Characteristically, Imamura focuses not on the leaders of the country, but on characters in the lower classes and on the fringes of society.

A tragic love story involving the 5th Shogun of the Tokugawa dynasty and a woman who became one of his concubines.