The first of the 13 ninja of the Koga society is dead after challenging Shintaro to a fight. Now Shintaro and his young companion,. Shusaku, are in search of another challenger.

While walking along a dusty road on their way to Kofu, Shintaro and Shusaku notice an express courier in a great hurry and they catch sight of a ninja knife falling out of his pocket. That night Shusaku is kidnapped.

While he and his companions are resting in an inn, Shintaro sees a scared rat running from the closet and realises there is someone hiding inside.

When the leader of the infamous Koga society harangues Kurobei for failing to rescue another ninja from Shintaro, Kurobei decides to turn against the society and join the master swordsman.

After sneaking out of a temple in which Shintaro has sought refuge for the night, Kurobei is challenged by a black clad figure in the belfry.

Shintaro goes to the rescue when he sees a band of villainous sedan-chair carriers running off with a girl named Chikage. Then he decides to help her locate her father.

Shintaro and his young companion have finally arrived in Kofu after many adventures but their arrival is being observed from afar by Sarobei and Genzo, two more master ninja.

The Koga ninja has been committing a series of crimes including arson and murder with the sole purpose of coaxing Shintaro into the open so he can be their next victim.

Ninja Kogento enables an expert rifleman to do away with Shintaro.

Shintaro offers to escort some fugitives from the Koga ninja into Kofu though this means he will have to walk back towards his enemies who are pursuing him.

While searching for a secret entrance to a hidden gold mine, Shintaro sees a group of ninja attacking a woodsman.

Shintaro and Shusaku, while journeying through the mountains, save the life of a farmer who is hanging upside down in a tree. He tells them he was attacked by the Koga and Shintaro realises they are nearby.