When a five-year boy, Ietsuna, suddenly becomes the Shogun of Japan, numerous schemes to seize his power begin to hatch.

Under orders from the Kouga clan, a revenge-seeking female ninja, Okou, infiltrates the bathhouse that doubles as the Shadow Warrior's secret base; meanwhile, a wild Iga ninja causes trouble for Hanzo by refusing to remain in hiding.

A minor clan comes to Edo looking for warriors to help them take over a castle.

After several loyal court nobles are brutally murdered, Hoshina suspects a plot against the government is brewing in Kyoto.

Under the guidance of a ninja hunter, the Tokushima clan is secretly gathering weapons and plotting a rebellion against the government.

The Iga ninja of Nagasaki are accused of running an illegal opium ring to help fund a campaign against the government; Hanzo and the Shadow Warriors venture to Nagasaki's foreign quarter to try and prove their clan's innocence.