3X3 Eyes tells the story of Yakumo Fuuji, a young man who, through a bizarre sequence of events, becomes the immortal servant of the last member of a race of three-eyed demons. To save his life, the demon absorbs his soul, thereby granting him immortality. He then embarks on a journey with the female demon, seeking a way to regain his humanity. The path is fraught with complications, most notably the demon's split personality—one side achingly cute, the other a force of no-nonsense destructive power—and the romantic entanglements that arise between them.