Le seigneur de guerre Oda Nobunaga vainc rapidement ses ennemis dans sa quête de pacifier et d'unifier le pays sous son autorité. Il existe cependant une région que lui-même craint : la province d'Iga où vivent les ninja de l'école Iga-ryū, connus pour posséder des armes de guerre extraordinaires, ne pas penser comme des humains et assassiner pour de l'argent. L'un de ses ninjas, Mumon, reconnu comme un assassin exceptionnel et qui n'a pas d'égal au combat, a gagné le surnom de « ninja le plus fort d'Iga ». Il est cependant également paresseux et cherche seulement à gagner de l'argent pour plaire à sa femme, Okuni. Dans le même temps, un ninja nommé Heibee Shimoyama devient désabusé par la manière de vivre de son peuple.
In a flashback, Hiko Seijūrō finds young Shinta digging graves for bandits and slavers killed in battle. Shinta explains that all people are only bodies after death. Hiko decides to take Shinta as his student and names him "Kenshin". Kenshin wakes up at Master Hiko's home, and asks if his friend (Kaoru) was also washed up. He has been unconscious for three days, and master tells him that his friend is most likely dead. Kenshin asks to learn the final Hiten Mitsurugi technique, "Amakakeru Ryu no Hirameki", in order to defeat Shishio Makoto and prevent his onslaught. Hiko agrees, and the two engage in a duel to start his training.
Kenshin has settled into his new life with Kaoru and his other friends when he is approached with a request from the Meiji government. Makoto Shishio, a former assassin like Kenshin, was betrayed, set on fire and left for dead. He survived, and is now in Kyoto, plotting with his gathered warriors to overthrow the new government. Against Kaoru's wishes, Kenshin reluctantly agrees to go to Kyoto and help keep his country from falling back into civil war.
A retired samurai must redeem himself for a crime that he committed earlier in his life. A squire is sent by the prime minister of Japan to keep watch over him.
In late medieval Japan, Kai (Keanu Reeves) is a half-Japanese, half-English outcast who lives in the Akō Domain, which is ruled by the benevolent Lord Asano Naganori. When Kai was young, Asano found him lost in the forest and accepted him into his household. Kai and Asano's daughter, Mika, eventually fall in love despite Kai being scorned by her father's samurai due to his lowborn status and mixed ancestry.
In 1945, Logan is held in a Japanese POW camp near Nagasaki. During the atomic bombing of Nagasaki, Logan rescues an officer named Ichirō Yashida and shields him from the blast.
As the Imperialist forces celebrated their victory in the Battle of Toba-Fushimi, the participant Hitokiri Battōsai walks away from the battlefield, abandoning his sword. But, the Battōsai's old katana is not left alone. It is claimed by one of the fallen, Udo Jin-e.
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.
Le samouraï Sakunosuke Inui reçoit l'ordre du chambellan de son clan de tuer un autre samouraï, Sakuma Morie, le mari de sa propre sœur. Mais celle-ci est décidée à protéger son mari coûte que coûte...
Attacked and wounded by a group of traitorous Japanese ninja, a mercenary samurai named Yamada (Ozeki) is rescued and nursed back to health by a group of Siamese warriors, in service to the King of Ayothaya. Confused by the mysterious identity of his assailants, Yamada stays with the warriors, befriending them, learning their art, and eventually pledging his loyalty and life to their cause and kingdom.
In the 1840s, Japan, as the Tokugawa Shogunate faces extinction, a corrupt lord named Matsudaira Naritsugu of Akashi freely rapes, tortures, and murders his own citizens. He is protected because the Shogun is his half-brother. However, the Justice Minister realizes the threat he poses if Naritsugu should further ascend, and hires a trusted older Samurai, Shinzaemon, to ambush and murder Naritsugu. Unfortunately, the conversation is overheard by the Samurai Hanbei, a childhood friend of Shinzaemon who has persisted in loyalty toward Naritsugu.
The films starts with young Ichi's wife (Satomi Ishihara) being murdered by Toraji (Sosuke Takaoka), the cowardly art loving son of a yakuza boss. Following her death, Ichi (Shingo Katori) returns to his hometown, where he hopes to resume a normal life under the guise of farmer with his friend Ryuji (Takashi Sorimachi). However, the same group of yakuza plan to change Ichi's hometown into a harbor, and start exploiting local peasants for money. Ryuji's land deeds are taken and ransomed at a high price, so Ichi uses his gambling skills to win the money for the deeds. This unveils his identity as the infamous Zato Ichi which the Yakuza don't like and burn down the house. The villagers draft a Tanran scroll to present to a passing official asking for assistance. However having Zato Ichi, a wanted criminal, in the village would not work in their favor so they devise a plan to dispose of him. They give him a blank scroll to "deliver" to the officials and lead him on a dangerous path sending the yakuza after him. However, he realizes it is the wrong path and makes it to the officials. His betrayal is revealed when he shows the blank scroll to the officials and they are insulted and leave. Ichi takes the responsibility of getting rid of the yakuza on himself, going to the yakuza headquarters and killing the boss. However he is shot by Toraji and stabbed by one of the Yakuza minions. Crawling on hands and feet he goes to the beach where he presumably dies reuniting with his wife in the next life.
A young woman on a train eyes a nervous man. In a flash, he is chased down the train and the young woman slices him in half. She is Saya (Jun Ji-hyun), a four-hundred-year-old skilled half human-half vampire samurai who hunts vampires. Raised by a man named Kato (Yasuaki Kurata), she works loosely with an organisation known as "The Council", a secret society that has been hunting vampires for centuries. Saya's motivation goes beyond duty; she wants revenge; Onigen (Koyuki), the oldest of the vampires, murdered her father. For her next mission, she goes undercover as a student at Kanto High School on an American air base near Tokyo, Japan.