A decade after the catastrophic ninja war that saw the rival Iga and Koga clans annihilate each other in a brutal contest to determine the Tokugawa shogunal succession, the few survivors have settled together in a hidden village. In the relatively peaceful Kan'ei era, the clans' once-ferocious rivalry has officially ended, but an uneasy tension persists. To preserve their bloodlines and secure their future, the elders arrange a formal union between the two young clan leaders: Koga Hachiro, the head of the Koga Five Treasures, and Iga Hibiki, the leader of the Iga Five Blossoms. Both Hachiro and Hibiki have inherited powerful eye techniques from their parents—Hachiro wields a spear-eye technique that can pierce and destroy, while Hibiki commands a shield-eye technique that blocks and nullifies. It is believed that if the two join together, an unknown and immense power known as Ouka, or the Cherry Blossom, will be awakened. They train diligently for this purpose, but their seemingly fated match is complicated by a hidden truth: Hachiro and Hibiki are not merely betrothed; they are twin brother and sister, born of the same blood.

Their fragile peace is shattered when a mysterious and inhuman group called the Jojinshu, led by a figure named Jonin, attacks the hidden village. The Jojinshu seek the power of Ouka for their own ends. Hibiki is captured and her body is torn apart, then turned into a puppet under Jonin's mind-control sorcery. Hachiro barely escapes with the help of his comrades. Six years later, having disbanded the ninja forces but continued his training, Hachiro is approached by representatives of the Tokugawa shogunate, including the monk Tenkai and the swordsman Yagyu, who seek the aid of the Koga and Iga to eliminate the Jojinshu and restore the shogunate's authority. Hachiro gathers eight surviving ninja from both clans and embarks on a mission to infiltrate the Jojinshu's mobile fortress, the Hororensha, to defeat Jonin's lieutenants, retrieve Hibiki's scattered limbs, and save her.

The narrative unfolds across several major arcs. First is the initial assault and defeat, where the Jojinshu overwhelm the village and Hibiki is taken. This is followed by a six-year period of regrouping and training. The central arc is the infiltration of the Hororensha, where Hachiro and his allies fight through the fortress's five levels, each guarded by a powerful Jojinshu lieutenant with unique supernatural abilities, such as a summoner of demonic beasts, a warrior with future sight, and a four-armed guardian. During this journey, the deepest secret of Hachiro and Hibiki's origin is revealed through a borrowed eye technique and illusion magic. In the final moments of the original ninja war, the dying lovers Koga Gennosuke and Iga Oboro wished for a peaceful future and for their love to bear fruit. This wish activated the power of Ouka, warping reality to create a world where Gennosuke and Oboro had children—Hachiro and Hibiki. They are thus anomalies, beings who should not exist in the normal flow of history, born from a single desperate wish. Hachiro resolves to honor the will of his parents and protect this fragile peace. After retrieving all of Hibiki's parts, she is revived, and together they confront Jonin in a final battle for the fate of the ninja clans and the power of Ouka.