On a Tokyo street at midnight, a lonely courier carrying gold belonging to the Shoguns minister is robbed and murdered by a mysterious figure that seemingly springs from the darkness. The courageous Shintaro investigates, only to discover the involvement of the Koga Ninja, who are eager to get their hands on gold to fund their empire of crime and tyranny. With deadly ninja lurking behind every corner, Shintaro finds himself in his most dangerous adventure yet! Set in Kai Province (Yamanashi Prefecture), the KOGA NINJA story also introduces audiences to Shintaro's boy companion Kurobei who is himself allied with the rival Koga Ninja!