The tale takes place around 1650, after the death of the third Tokugawa shogun, when ronin were expelled from Edo, the military capital. During the political instability following the death of Iemitsu Tokugawa, Hanzo's Iga ninja clan battles against the Koga clan as various factions vie to seize power. The child shogun Ietsuna is kidnapped but turns out to be hidden under (or over) everyone's noses in a castle turret which is reinforced by a comic book villain, the fire-spitting black ninja. The good ninja has to get through all the traps & save the child.

徳川三大将軍家光の死後、世継ぎをめぐる幕府の争いはそのまま伊賀と甲賀、忍びの二大勢力の争いへと直結。「下」の服部半蔵は、伊賀忍者の復権を目論む「上」の服部半蔵の野望にやむなく協力し、甲賀四郎兵衛ら甲賀忍軍と対峙することになるが…