In the year 1651, 11-year-old Tokugawa Ietsuna is installed as the fourth Shogun of the Tokugawa Era, sparking the enmity of various clans and officials who continually plot to gain more power. Fearing the potential for civil war and instability in the land, the Hattori Family of Ninja is called upon to resume their traditional role as protectors of the Shogun. Hailing from the powerful Iga Clan of Ninja, and led by the skilled Hattori Hanzo, they masquerade as ordinary citizens during the day. But at night, they emerge as Kage no Gundan, the secret Shadow Army of the Shogun.