Through a strange series of events, a young man named Yakumo Fuuji becomes the immortal slave of the last of a race of 3 Eyed immortals. The immortal, Pai, absorbs his soul to save his life, making him immortal in the process. Now, he begins a journey with the female immortal in an attempt to find a way of becoming human. Of course, there are many complications along the way, not the least of which being that the immortal is a female with a split personality, one achingly cute and the other being no-nonsense destructive power, and romances that develop between.

3x3 Eyes was partially published in English by Dark Horse Comics from March 1, 1995 to May 5, 2004. The publisher discontinued the publishing of the manga after volume 8.