A cowardly samurai is sent as an official executioner targeting the clan's former sword instructor, a man whose sword and spear skills are second to none.

Unusual volcanic activity in Japan awakens Gyaos, a bloodthirsty flying monster with the power to slice things in half with an ultrasonic ray. While scientists and the military scramble to devise a way to stop this new threat, a young boy forms an alliance with Gamera; a monster no one else seems to trust.

Zatoichi, the famed blind swordsman, returns to his home village for the first time in many years. He is befriended by Omiyo, who had the same wet-nurse as Zatoichi. He also encounters a boyhood friend, Shinbei, who now is wealthy and appears not to remember Zatoichi. Shinbei seems to be interested in repaying the villagers' debts, but is in reality manipulating the ownership of a now-valuable rock quarry. Zatoichi learns of the subterfuge and confronts his old friend, who has a score of yakuza swordsmen backing his play.

All is not well in the medieval Kingdom of Koryo (918-1392), a distant precursor of today's Korea, ruled over by a corrupt dynasty in the north. While the Koryo overlords become bloated on a lifestyle of luxury and decadence, a series of farmer’s revolts rock the country, only to be mercilessly quashed. During one such uprising, the parents of a young girl, Somi, are ruthlessly murdered by the brutal government vassal Hyon Ryu Bal. The shock causes Somi to lose her voice, as she flees by boat for her life. She is rescued and taken in by Dosa, a white-haired martial arts master, along with another young boy from Somi's village, Ung Gom, orphaned in the same raid. As Dosa raises the two in his martial arts school, Somi and Ung Gom grow up together like brother and sister, waiting until their day of vengeance arrives.