In an era when ninjas were revered as semi-divine rulers who maintained peace in Japan through their martial mastery, a forbidden hara-kiri ritual was performed by certain individuals, allowing their souls to be preserved at Kinkaku Temple for eventual resurrection. Over time, the true history of these ninjas faded into obscurity. Fast forward to a future dominated by advanced cybernetics and digital networks, where the souls of ancient ninjas have returned to haunt the shadows of Neo-Saitama. Fujikido Kenji, an ordinary office worker, witnesses his family tragically killed in a ninja conflict. As he approaches death, Kenji is overtaken by a mysterious ninja spirit. Reborn from this ordeal, he becomes Ninja Slayer, a vengeful hunter on a mission to eliminate malevolent ninjas while seeking personal justice. In the grim underworld of Neo-Saitama, Ninja Slayer battles the evil ninjas of the Soukai Syndicate.