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.
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.
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 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.
Gennosuke is a rebel samurai on the run, having fled his clan after assassinating a counselor. The daughter of the counselor, Misa, and her fiance, Daizaburo, pursue Gennosuke along with other samurai from Gennosuke's clan despite Gennosuke's obvious superiority as a warrior. A series of flashbacks reveals that Gennosuke was manipulated into committing the treason by one of the clan's higher-ranking samurai, who led Gennosuke to believe that the counselor's death would result in modern reforms to the clan and in Gennosuke's promotion to a full-fledged retainer, instead of a lowly foot soldier. In fact, the ranking samurai simply wanted the counselor killed so that he could succeed to the position himself. He had used Gennosuke to do the "dirty work", and then abandoned Gennosuke to face the consequences of the crime.
Oyuki, a tattooed female assassin – the renegade member of a daimyo's personal bodyguard detail – is killing every man that is sent up against her. Along with her deadly use of the short blade, she strips to the waist while fighting to reveal elaborate tattoos on her chest and back. On her front is a kintarō grasping her left breast. A portrait of a mountain witch covers her back. She then cuts off her victims' topknots, or chonmage, which brings dishonor to the dead man and his family.
Ogami is tested by five messengers, each who try to kill him. After defeating all the messengers, Ogami learns he must kill a young girl who was raised as a boy and is intended to be the heir of a local daimyo, while the real heir, a little boy, is kept locked away. In addition to murdering the senile, old lord, his concubine and the girl, Ogami must stop a document revealing the deception from reaching the hands of his mortal enemy, Yagyū Retsudō. Meanwhile, Ogami Daigoro is again separated from his father and proves his courage and sense of honor as he refuses to admit the guilt of a woman pickpocket he became mixed up with.
Ogami Ittō, the disgraced former shogun's executioner, or Kogi Kaishakunin, is traveling by river on a boat with his young son Daigoro floating behind in the baby cart. A young woman at the front of the boat, clearly distraught for some reason, accidentally drops a bundle into the water, which Daigoro retrieves. Ittō, draws his sword partway and notices in the reflection on the blade that some bamboo reeds are trailing the boat. Ittō is being followed by operatives of his mortal enemy, the Yagyū Clan – a constant threat that he can never ignore. Later, as Daigorou is relieving himself in a bamboo glade, Ittō slices some bamboo stalks, causing some ninja to fall from their perch.
In a town dominated by yakuza, Zatoichi (Katsu) encounters a master swordsmith named Senzo (Tōno) who identifies Zatoichi's cane sword as the work of his late mentor. Senzo also spots a crack in the blade and warns that it will snap after one more kill.
A group of assassins stop a blind men pilgrimage making their way down the road. The assassins ask for Ichi, but they all claim variations of that name. They line them up against a building to look at their faces, but do not find Ichi and leave. One of the blind men brings Ichi out from his hiding place in the building, and they laugh at playing a prank on sighted men. Ichi goes on his way.
Zatoichi (Katsu) checks into an inn where he shares a room with an ill woman and her young son named Ryota. Before the woman dies, she requests that Zatoichi take her son to his father, an artist living in the nearby town of Maebara.
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.
The film tells the story of two Shinsengumi samurai. One of them is Saitō Hajime (played by Kōichi Satō), a heartless killer and the other is Yoshimura Kanichiro (played by Kiichi Nakai), who appears to be a money-grubbing and emotional swordsman from the northern area known as Nambu Morioka. The main storyline is set during the fall of the Tokugawa shogunate, but it is told in a series of flashbacks as two characters reminisce. The themes include conflicting loyalty to the clan, lord, and family.
Following the battle of Sekigahara, Takezo (Toshiro Mifune) and his friend Matahachi (Rentarō Mikuni) find themselves on the losing side. Instead of the grand victory and glory Takezo had anticipated, he finds himself a hunted fugitive, having to assist a severely injured Matahachi. The pair seek shelter with a widow and her daughter who unknown to them are connected to local brigands. The brigands soon show up and ask for tribute from what the women have stripped off dead samurai, and Takezo has to fight them off. Both women attempt to seduce Takezo but are rejected. The widow then tells Matahachi that Takezo tried to assault her and convinces him to escort her and her daughter to Kyoto. Matahachi agrees even though he loves (and is betrothed to) Otsu (Kaoru Yachigusa), a woman from his village.