The lead character in 3X3 Eyes is Yakumo Fuuji, who finds himself intertwined with a powerful demonic entity possessing three eyes, granting it immortality. Following a peculiar series of events, Yakumo's soul is absorbed by the demon, granting him immortality as well. Their mission is to undo Yakumo's transformation, but they encounter several difficulties, such as dealing with the female demon's split personality - one charming and warm, the other violently aggressive - as well as navigating romantic complications.