The story is set about 10 years after the events of the original series. The protagonist, Shinichi Kuruma, has been forcibly transformed into a "majuu" (a beast-human hybrid) by his father, Genzou Kuruma, a mad scientist seeking to evolve humanity. Shinichi embarks on a quest for revenge, not only against his father but also against the 13 Apostles, who are other powerful hybrid beings, and a cosmic entity called Tokitenkuu, which threatens the fabric of space and time.