In the year 1844 of the Edo Period, as the Tokugawa Shogunate is in decline, the sadistic Lord Matsudaira Naritsugu of Akashi rapes, tortures, mutilates and murders nobles and commoners at will. He is shielded because the Shōgun is his half-brother. Sir Doi Toshitsura, the Shōgun’s Justice Minister, realizes that when Naritsugu ascends to the Shogunate Council, civil war will break out between the Shōgun and the many feudal lords Naritsugu has offended. Then, the feudal lord of the Mamiya clan publicly commits ritual suicide by disembowelment as a protest against the Shōgun’s refusal to punish Lord Naritsugu, who has personally murdered the feudal lord’s entire family. When the Shōgun still insists upon Naritsugu’s promotion, Sir Doi seeks out a trusted older samurai, Shimada Shinzaemon, who served under the former shōgun, and secretly hires him to assassinate Naritsugu. However, Naritsugu’s loyal retainers led by Hanbei, an old contemporary of Shinzaemon, learn of the plot by spying on Doi.
Shinzaemon gathers eleven trusted samurai including Shinzaemon’s nephew, Shinrokurō, who together plan to ambush Naritsugu on his official journey from Edo to his lands in Akashi. Just before they leave, Hanbei arrives and warns his old colleague that he will suffer grave consequences if he tries to kill Naritsugu.
The group, with the legal authority and financial assistance of Doi, buy the help of the town of Ochiai in order to create a trap. They also enlist the help of Makino, a feudal lord whose daughter-in-law was raped and son murdered by Naritsugu. With troops, Makino blocks the official highway, forcing Naritsugu to head into the trap; Makino then disembowels himself to conceal his own involvement in the conspiracy. During the assassins’ journey to the town, they are attacked by masterless samurai who have been paid off by Hanbei to kill the plotters. The group decides to head through the mountains but end up getting lost. In the process they encounter a hunter named Kiga Koyata who becomes their guide and later the thirteenth assassin.
The town is converted into an elaborate maze of booby traps and camouflaged fortifications. When Naritsugu and his retinue arrive, their numbers have been augmented by additional troops. The 13 assassins are no longer facing 70 men-at-arms; now they face at least 200. A lengthy battle follows, with Naritsugu and his guards trapped inside the village and attacked on all sides by arrows, explosives, knives, and swords – with the exception of Koyata, who fights with rocks in slings and with sticks. In the midst of the carnage, the sadistic Naritsugu is aroused by the bloodshed of the battle. He tells Hanbei that when he ascends to the Shōgun’s council he will bring back the wars of the Sengoku Period.
The assassins are killed one by one, but not before they kill nearly all of the Akashi forces. Eventually, Naritsugu and Hanbei are cornered by Shinzaemon and Shinrokurō. After Shinzaemon kills Hanbei, Naritsugu kicks his loyal retainer’s head away, insulting the samurai who has given his life for him. Contemptuously, he announces that the people and the samurai have only one purpose: to serve their lords. Shinzaemon counters by telling Naritsugu that lords cannot live without the support of the people and that, if a lord abuses his power, the people will always rise up against him. Naritsugu and Shinzaemon mortally wound each other. Crying, crawling in the mud, and experiencing fear and pain for the first time, the lord thanks Shinzaemon for showing him excitement. Shinzaemon then decapitates him.
Shinrokurō wanders through the carnage and meets the hunter Koyata who, having suffered a fatal injury earlier, runs up to him with characteristic vigor, unharmed. They make their separate ways out of the town after they briefly discuss how they intend to live their lives from then onwards. An epilogue states that the Shōgun and his government covered up what really occurred, announcing that Naritsugu died of illness on the journey back to his lands. Twenty-three years later, the Tokugawa Shogunate would be overthrown during the Meiji Restoration.