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.

In order to save the daughter of Kuroiwa clan lord who was made ill by the curse of someone, Hattori Hanzo brings the shadow warriors.

The monster Zippo, who had an ominous prophetic dream and came to Tokyo worried about his childhood friend Hattori-kun, witnessed countless pink eggs raining down from the sky. It is the egg of a monster sent by invaders who are trying to consume the earth's plants for energy. Hattori-kun and his friends struggle to repel them with the help of Perman who rushes in?