Le Japon en 1860, à l'aube de l'Ère Meiji. Un groupe d'assassins a pour but d'éliminer un personnage important du pays. Ils suspectent la présence d'un traître parmi eux, et leurs doutes tombent sur Niiro, un ronin, et son ami Kurihara l'aristocrate.
Tatsuya Nakadai stars as Genta, a former samurai who became disillusioned with the samurai lifestyle and left it behind to become a wandering yakuza (gang) member. He meets Hanjirō Tabata (Etsushi Takahashi) a farmer who wants to become a samurai to escape his powerless existence. Genta and Tabata wind up on opposite sides of clan intrigue when seven members of a local clan assassinate their chancellor. Although the seven, led by Tetsutarō Oikawa (Naoko Kubo) rebelled with the support of their superior, Ayuzawa (Shigeru Kōyama), he turns on them and sends members of the clan to kill them as outlaws.
À la suite d’un ordre secret émanant d’un haut dignitaire du shogunat Tokugawa, 13 hommes ont un objectif commun : assassiner Matsudaira Nariaki, le daimyō du clan Akashi, un homme sanguinaire et despotique, devenu incontrôlable. Ils ont soixante jours pour réussir cette mission suicidaire…
The samurai Sakawa Kojūrō is on the road to Edo with his two servants Genta and Genpachi. Kojūrō is a kindly master, but his character totally changes when he consumes alcohol. On the road, they encounter many different people: a traveling singer with her child, a father taking his daughter Otane to be sold into prostitution, a pilgrim, a policeman searching for a notorious thief, and Tōzaburō, the suspicious man the officer has his eyes on. Genpachi, the spear carrier, is also followed by an orphaned boy named Jirō who wants to be a samurai. When Kojūrō and Genpachi inadvertently capture the thief—who was the pilgrim in disguise—Kojūrō is disgusted when the authorities praise him and not his servant, even though Genpachi probably contributed more. He is also upset that he does not have the money to save Otane from being sold. In the end it is Tōzaburō who saves Otane, using the money he saved to rescue his own daughter, but decided to use for Otane after finding out his daughter had died. Depressed, Kojūrō takes Genta out drinking, despite the protests of the latter. When a band of boisterous samurai complain of Kojūrō drinking with someone of lower birth, Kojūrō gets upset. The samurai pull their swords and kill both the servant and his master. Genpachi arrives too late, but in a fury kills all the samurai with the spear. Authorities do not charge him with a crime, so he heads home carrying the ashes of Kojūrō and Genta. When Jirō tries to follow him, he shoos him off, telling him never to become a samurai.
Okada Izo is a ronin born into poverty who joins the Tosa loyalists, a group headed by Hanpeita Takechi. Izo soon becomes a well known and successful killer, and he is stubbornly loyal to Takechi. However, Ryoma Sakamoto warns him that he is merely "Takechi's dog" and that Takechi will end up betraying him. As Takechi becomes more and more determined to succeed, it becomes necessary to sacrifice Izo, which he does by having him arrested and later trying to poison him. Izo, disillusioned, confesses to his murders for the Tosa Loyalists, and he is condemned to Crucifixion. Before being killed, he is told that Takechi will be forced to commit seppuku.
Hanshiro, un samouraï sans ressources, demande au clan Ii l'autorisation de commettre le suicide rituel des samouraïs (Seppuku) au sein de leur résidence. Il est reçu par l'intendant Kageyu qui tente de l'en dissuader en lui racontant l'horrible histoire d'un jeune rōnin qui s'était présenté à eux avec la même demande.
Following Takezo's (Toshiro Mifune) capture by the Buddhist priest Takuan Sōhō, and stay in Himeji Castle. Takezo is granted his samurai name 'Musashi Miyamoto.' and leaves to search for enlightenment, leaving two messages for Otsu: "Soon I will be back" and "Forgive me." He goes to learn the way of the samurai and find those who will help him learn. But his first duel is with a challenger with a chain and a sickle who he fights and wins. After years on the road establishing his reputation as Japan's greatest fencer, Takezo travels to Kyoto. The now married Matahachi and Oko are settled there with Akemi. Otsu, having heard a rumor that Takezo is in Kyoto, has also travelled there to look for him. He meets Otsu who is in love with him but he tells Otsu he must follow what he loves more than her, the sword of the samurai.
As the opening credits roll, an abbreviated version of Ogami Ittō's (Tomisaburô Wakayama) past as Shogunate Decapitator and his wife's murder by ninja are seen, with Daigorō (Akihiro Tomikawa) providing the narration.
The swordsman Ogami Ittō is confronted by a secretive branch of the Yagyū clan that practices black magic, including the ability to burrow through the earth. He encounters Kaori, a female expert with knives. And there's Hyouei, an illegitimate son of Yagyū Retsudo who kills anyone Ittō and Daigoro come into contact with. It culminates in a final battle between Ittō and the combined clan groups under Retsudo on a snow-capped mountain in northern Japan, in which the baby cart becomes a sled. Ittō defeats the entire army, shooting, stabbing, slashing, dismembering, and beheading the entire army. But the one-eyed Retsudo again gets away, vowing to kill Ittō another time.
Ichi travels to his old village four years after he stopped training. On the way he meets his childhood friend Tamekichi. Tamekichi, his wife and child have become poor, and must make a living with music. While at an inn, a group of travelers are robbed by four thieves but Ichi does not stop them.
It is set during the last days of the Shogunate. Saheiji (played by comedian Frankie Sakai) seeks to outwit the inhabitants of a brothel in order to survive in straitened times. A group of samurai meanwhile seek to destroy any foreigners that cross their path.
Ichi travels to the village of Itakura to pay respects at the grave of a man he killed two years earlier. At the grave he reminisces on a fight between the two yakuza gangs (Iioka and Sasagawa from an earlier film) one man ran away and, though Ichi was not taking part in the fight, attacked Ichi. The dead man's sister, Chiyo, overhears Ichi say this to himself.
Zatoichi comes to a village which is the local hub of family farms in a silk growing region. The most prominent villager is Matsugoro who apparently will stop at nothing to bring all under his control. The small village does have a kind doctor, Dr. Junan, who lives with his daughter Oshizu.