A young boy named Yaiba Kurogane has spent his entire life training in a remote tropical jungle with his father, Kenjuro, striving to become a true samurai with no knowledge of the modern world. Their secluded life ends abruptly when they accidentally hide inside a cargo container that gets shipped all the way to Japan. Upon arrival, they encounter the Mine family, led by Kenjuros old rival Raizo, and his daughter Sayaka. Yaiba agrees to a deal to stay with them, quickly proving his extraordinary strength by defeating the strongest student at their dojo.

Eager to test his skills against powerful opponents, Yaiba follows Sayaka to school, where he meets a kendo prodigy named Takeshi Onimaru. Their fierce clash ends in a stalemate, but the humiliation of not achieving a decisive victory drives Onimaru down a dark path. He discovers an ancient, malevolent katana hidden beneath his family home, the Fujinken or Sword of the Wind God. Upon taking the blade, Onimaru is possessed by its demonic power, transforming into a demon lord bent on conquering Japan with an army of monsters.

To counter this threat, Yaiba must find the legendary counterpart, the Raijinken or Sword of the Thunder God. His search leads him to the legendary swordsman Miyamoto Musashi, who, despite appearing as a lecherous and gluttonous old man, becomes Yaibas mentor. With the Raijinken in hand, Yaiba begins a quest to master its lightning powers, facing Onimarus Eight Demons and other mythical foes.

Throughout the journey, Yaiba is joined by a colorful group of allies, including Sayaka, his cowardly pet tiger Kagetora, and his vulture Shonosuke. Several of Onimarus resurrected minions, such as the frog warrior Gerozaemon and the legendary swordsman Sasaki Kojiro, eventually switch sides and join Yaibas cause. The narrative follows Yaibas growth from a wild jungle boy into a hero, encountering numerous figures from Japanese history and mythology.

The story progresses through several major arcs. After storming Onimarus fortress and forcing him to retreat, the conflict escalates when a floating castle appears, prompting a quest for seven legendary orbs to summon the Dragon God Ryujin. Later, the awakening of Ryujins power draws the attention of the Moon Princess Kaguya, an alien menace that Yaiba must seal away. Subsequent adventures include exploring a mysterious pyramid causing earthquakes, battling the forces of the Underworld, and finally confronting the demon Yamata-no-Orochi unleashed by Onimaru.