Yakumo Fuji was an average boy living on his own, until he runs into a girl named Pai. He later finds out that Pai is the last survivor of a mythical Triclop race known as the Sanjiyan Unkara. He also finds out that his father, Professor Fuji, had promised Pai that he would help her become a normal human being. Pai had met Professor Fuji during his expedition in the Himalayas, in his quest to uncover the truth about the Sanjiyans. During the expedition Professor Fuji fell ill and passed away. But before he died he told Pai to find his son who would help her find the Ningen no Zou, the Statue of Humanity, which has the power to turn her into a human.
On the night of their meeting, Yakumo is accidentally killed by Takuhi, a spirit that lives in Pai's walking stick. In order to save Yakumo's life, Pai took Yakumo's soul and merged it with her own. From then on Yakumo is left with the sign of the void upon his forehead and is given immortality. Yakumo now has no choice but to help Pai become human, since it's the only way for him to get his soul back. The Statue of Humanity is also wanted by a mysterious cult who require the Ningen no Zou so that they can raise their dark lord Kwia-Yan-Wang. Yakumo is thrusted into the supernatural world of monsters and demons, in order to help Pai become human and get his life back to normal again.
Series 2
The second series of 3x3 Eyes continues Pai's and Yakumo's journey to become human. It takes place four years after the first series. Ayanokouji Pai believes she is an ordinary high school girl with friends and a normal life in Tokyo. That is until she runs into Yakumo, who had been looking for her for four years. Pai had forgotten about her past and who she really is, the Sanjiyan within her has been kept asleep and dormant all that time. Yakumo tries must convince her about her other life and that she isn't a normal human, but when he speaks of demons and monsters, Pai doesn't believe him. She begins to believe when they are attacked by the demons responsible for keeping her past life a mystery. To gain her memory back she decides to join Yakumo and travel to the Himalayas to uncover her past. And so the journey of Yakumo and Pai continues, but this time they are not looking for Pai to become human, but for Pai's long lost memory, about the past events that occurred in Hong Kong and further back to the time when Kwia Yan Wang reeked havoc and destruction on Earth, during the Sanjiyan War, 300 years ago.