In 1876, U.S. Army captain Civil War veteran Nathan Algren is traumatized by his participation in atrocities during the Indian Wars, and has become an embittered alcoholic. Algren is approached by his former commanding officer, Colonel Bagley, on behalf of Japanese businessman Omura, who wishes to hire distinguished U.S. soldiers to train the Imperial Japanese Army to suppress a samurai rebellion, led by Katsumoto Moritsugu. In exchange, Japan would ratify a lucrative trade agreement that would grant the U.S. exclusive rights to supply arms to the Japanese government. Although Algren despises Bagley for having ordered atrocities during the Indian wars, he accepts the job for the money and sails to Japan. Most of the soldiers being trained are little more than inexperienced peasants and farmers.The training is interrupted when the samurai rebels attack a railroad owned by Omura; Bagley orders the regiment to mobilize, overruling Algren's objection that the soldiers are not ready. Algren is proved correct: during a battle in a foggy forest in Yoshino Province, the undisciplined and intimidated soldiers panic and are quickly routed by the samurai horsemen. Algren kills several samurai with his revolver and saber but is eventually knocked from his horse. Algren desperately fights using a spear tipped flagstaff with a flag of a white tiger until he collapses from complete exhaustion. As he is about to be vanquished, he kills his would-be executioner with the staff's spear tip. His ferocity and refusal to surrender, as well as the image of the white tiger on the flag he is fighting with, reminds Katsumoto of a recurring dream. As a result, Algren is spared and taken captive to the rebels' village in the mountains.
A woman in a wedding dress, the Bride, lies wounded in a church in El Paso, having been attacked by the Deadly Viper Assassination Squad. She tells their leader, Bill, that she is carrying his baby. He shoots her.
The pregnant Bride and her groom rehearse their wedding. Bill, the Bride's former lover, father of her child, and leader of the Deadly Viper Assassination Squad, arrives unexpectedly. On Bill's orders, the Deadly Vipers kill everyone at the wedding, but the Bride survives and swears revenge.
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.
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.
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.
In feudal Japan 1603 (Late Sengoku period) a young man is being chased by four samurai on horseback. As they go into the woods, a mysterious woman emerges from the underbrush and watches closely. However, the samurai eventually capture and take the youth, revealed to be a prince named Kenshin, with them.
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.
Shinnojo, a low level samurai, lives with his pretty, dutiful and loyal wife Kayo. He has come to find his position in a castle as a food-taster for a feudal lord to be boring and pointless, and talks about opening a kendo school open to boys of all castes where he can teach the use of the sword. Before he can act on his dream he becomes ill with a fever after tasting some sashimi made from shell fish, but an investigation reveals that the poisoning was not due to a human conspiracy, but a poor choice of food out of season. After three days he awakes but finds that the toxin from the food has blinded him. Kayo is summoned by Shinnojo's family to explain how the couple will survive. His uncle laments that he no longer knows anybody with influence in the castle, and asks Kayo if she knows of anybody. She relates how Toya Shimada, the chief duty officer in the castle and a samurai of high rank, offered to help and they tell her to act upon his offer of assistance. A message from the castle brings the good news that Shinnojo's stipend of rice will remain the same, and for life but his aunt tells him that Kayo was seen with another man. He has Tokuhei, his faithful servant, follow her. Kayo notices that she is being followed, and although Tokuhei offers to cover for her, she reveals to Shinnojo that Shimada offered to help but with a price, shown when he forced himself upon her. He then solicited three additional trysts by threatening to tell Shinnojo about the first. An enraged Shinnojo divorces her and orders her out of his house. When it is revealed to him that Shimada had nothing to do with maintaining his stipend, but that it came out of gratitude from the lord of the clan himself, Shinnojo seeks to renew his skill with the sword as a blind man to avenge the dishonor of Kayo. Through Tokuhei, he sends a message to Shimada to set up a duel, with the additional message to not underestimate him. The two samurai meet at the stables near the river to decide their destinies. In the subsequent fight Shinnojo cuts off Shimada's arm. He leaves Shimada to live a horribly disfigured life, telling Tokuhei that he has now avenged Kayo's dishonor. The next day Shinnojo is informed that the injured Shimada refused to tell anyone what had happened or who injured him in the duel. That night Shimada committed seppuku and killed himself, as a samurai cannot live with only one arm. He dies without anyone knowing of his sin against the Mimura family, his violation of Kayo, or his own dishonorable injury by a blinded man. Tokuhei tells Shinnojo he has found a girl to work in the kitchen and cook for him. After one taste of the girl's food, Shinnojo recognizes his wife's cooking, and calls Kayo to come into the house. Shinnojo and Kayo reconcile, with an understanding that they will begin their life together anew.
The film's plot follows a traditional theme, with Zatoichi (a blind swordsman) coming to the defense of townspeople caught up in a local Yakuza gang war and being forced to pay excessive amounts of protection money. Meanwhile, Zatoichi befriends a local farmer and her gambler nephew and eventually offers his assistance to two geisha siblings (one of whom is actually a man) who are seeking revenge for the murder of their parents. The siblings are the only survivors of a robbery and massacre that was carried out on their family estate ten years ago. They soon discover the people responsible for the murders are the same Yakuza wreaking havoc on the small town.
Lord Shingen Takeda meets with his brother Nobukado, and a thief whom the latter met by chance and spared from crucifixion. Nobukado believes the thief's uncanny resemblance to Shingen would prove useful. The brothers then agree that he would prove useful as a double, and they decide to use the thief as a kagemusha.
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.
Ghost Dog (Whitaker) sees himself as a retainer of Louie (John Tormey), a local mobster, who saved Ghost Dog's life years ago. While living as a hired hitman for the Italian Mafia, he adheres to the code of the samurai, and interprets and applies the wisdom of the Hagakure in his contracts for the mob.
The film takes place in Japan in the 1860s, a time of cultural assimilation. Two samurai, Munezo Katagiri (Masatoshi Nagase) and Samon Shimada (Hidetaka Yoshioka), bid farewell to their friend, Yaichiro Hazama (Yukiyoshi Ozawa), who is to serve in Edo (present-day Tokyo) under the shogunate of that region. Though the position is desirable, Katagiri voices his concern that a man of Yaichiro’s character is likely to run into trouble. His doubts are assured when the married Yaichiro expresses an intention to indulge in Edo’s sensual pleasures while stationed there.