3x3 Eyes is the story of a young man named Yakumo Fuuji, who through a strange series of events becomes the immortal slave of the last of a race of 3 Eyed immortals. The immortal 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.
In the year 1600, during the battle of Sekigahara, warriors Kyoshiro Mibu and "Demon Eyes" Kyo, engaged in fierce combat. Both men disappeared when a meteor crashed in the battlegrounds. Four years later, Kyoshiro is spotted on a rural highway, acting as a traveling medicine salesman. He is captured by the female bounty hunter Yuya Shiina when she discovers that deep inside him is the dormant personality of "Demon Eyes" Kyo himself.
On the path of swordsmanship in a "Futuristic" yet Feudal Japan, it is said that the one who becomes No.1 will rule the world. But the only rule in this world is that only the No. 2 is allowed to fight the No. 1. The Afro Samurai who is the current No. 2, travels the road looking for revenge on the man who killed his father, a three-armed gunman who has harnessed god-like power and is the current No. 1.
Naota is a normal Japanese 6th grade boy, but when his older brother leaves for America to play baseball, he leaves his homeless 17 year old girlfriend Mamimi behind. Mamimi is sending mixed signals and advances to Naota, and he doesn't know what to do about her. But to make matters worse, Naota's world is totally turned upside down when he is run over by a woman on a Vespa.