Centuries ago, the ruthless feudal warlord Gengetsu Kibaoni was slain by the Igasaki Ninja clan, before discarding his humanity to become a Yokai. In his first attempt to rise again, Kibaoni was defeated and sealed by Yoshitaka Igasaki, a man known as the Last Ninja, but three generations later, Kibaoni is unsealed by his retainer Kyuemon Izayoi. As only members of Igasaki's bloodline can stop the rampaging Yokai, Yoshitaka's son Tsumuji Igasaki assembles the Ninningers, composed of his children Takaharu and Fuka and their friends Yakumo Kato, Nagi Matsuo, and Kasumi Momochi, to master their clan's Shuriken Ninja Arts (手裏剣忍法, Shuriken Ninpō) and fight the Kibaoni Army Corps. The team is later joined by Kinji Takigawa, a Yokai Hunter from the United States who becomes Yoshitaka's disciple after earning his trust. Also, according to their grandfather, one among them will be chosen to inherit the title of Last Ninja, and become the guardian of the Igasaki family's ultimate treasure, the "End Shuriken", which is also coveted by the Kibaoni Corps in their plan to revive their master and take over the world by fear.