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 the time of the peaceful Toyotomi Era, Shinotada, the master of Kochi Family, a source of revenue for the Tokugawa, is trying to marry his younger sister Princess Fuji to Akinobu Sunekazura, who has connections with the rival Toyotomi, in order to bring peace. One of sixteen great warriors of Tokugawa, Hattori Hanzo, entrusts his wish and gathers the remnants of Iga Village, which was destroyed by Oda Nobunaga, and orders them to guard Princess Fuji. The Council of Elders of Sunekazura, hire the Fuma Ninja led by Fuma Kotaro, joined by the Koga Ninja, led by Sarutobi Sasuke, who is serving Hideyoshi Toyotomi, to assassinate Princess Fuji! Can Hanzo Hattori with the Iga remnants prevent this evil plot and protect the princess? Once again, Shinichi "Sonny" Chiba plays the leading role of Hanzo Hattori with his old enemy, Sarutobi Sasuke, played by Hiroki Matsukata. The presence of both famous actors will overwhelm any audience!

Toyotomi Hideyori's married granddaughter, Princess Sen, is targeted by someone. Hattori Hanzo, who receives the news, challenges the blocking of conspiracy to recover Senhime.

Iga ninja led by Hattori Hanzo took back Princess Fuji who was kidnapped by Fuma Clan at the end of the war. However, there were three of them - one being the real Princess Fuji and the others doubles. Not knowing which is the real one, the Iga ninja has no choice but to separate into three teams to deliver the princess to her wedding. The evil hands of the Fuma and the Koga are trying to reach Princess Fuji and the Iga ninja. Their difficult journey has begun.

Shippuu (Hayate) appeared suddenly dead. However, he fell into the hands of Sarutobi for due to his loss of memory.

In the world of the Ninja, fighting skills play a small role in one's rank in the Shinobi order. Kageru is the best in his class, but his birth predestines him to the lower class. His friend Aoi is dealt the same fate; together they'll have to question themselves.