After nearly being slain by ninjas who also kill his wife and child, Fujikido Kenji seeks vengeance; he merges with the spirit of Naraku Ninja to become the Ninja Slayer, the ninja that kills ninjas.

After a massive drug deal is interrupted, Arson, one of the Soukaiya's ninjas, faces Ninja Slayer in a battle to the death; Ninja Slayer has his hands full while taking on a techno-ninja named Cloud Buster.

Kenji Fujikido is a salaryman whose wife and child were killed in a ninja turf war; in a brush with his own death, Fujikido is possessed by an enigmatic ninja soul known as Naraku Ninja; Fujikido cheats death and becomes Ninja Slayer.

After tofu manufacturing plant worker Shigaki loses his arm in an industrial accident, he joins other injured workers in taking revenge against the company; Ninja Slayer continues hunting for members of the Six Gates.

Under orders from Laomoto, Six Gates ninjas Earthquake and Hugeshuriken hunt for the Dragon Dojo, run by Dragon Gendoso; they intend to burn it down.