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.
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.
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.
Hidetora Ichimonji, a powerful warlord, experiences a dream reminding him that he's showing his age and decides to divide his kingdom among his three sons: Taro, Jiro, and Saburo. Taro, the eldest, will receive the prestigious First Castle and become leader of the Ichimonji clan, while Jiro and Saburo will be given the Second and Third Castles. Hidetora will retain the title of Great Lord and Jiro and Saburo are to support Taro.
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.