Fuma ninja clan is a secret ninja tribe that is waiting for the "Orochi" (gigantic snake) to resurrect for generations. Shirasu and his twin brother Ichiu grew up in this viscous environment and this tells how they become the leaders of the clan.

The three brothers discover that the human experiment banned after destroying the "Orochi", is still going on to secretly revive the evil snake. They also find out that some ex-members of the Yamainu (the Japanese military unit formed to kill the snake) are behind this conspiracy. The brothers fight together again in a battle against the military.

One year has passed after the great battle against the Orochi (gigantic snake). Tenka Kumo had been paralyzed from the final battle and he took part of the government’s human experiment before the battle. Tenka withdrew himself from society but his younger brothers Soramaru and Chutaro find out the secret past about their older brother.