Just like the first part, this game also takes place in feudal Japan, only this time around not only introducing the already well known pair of ninjas known as Rikimaru and Ayame, but a new comer by the name Tatsumaru. The three ninjas must protect Lord Gohda Matsunoshin against a mysterious group of ninjas calling themselves the Burning Dawn. It is up to them to put a stop to whatever the Burning Dawn clan have planned.