Ash Lynx is a beauty, a genius—and a murderer. Since childhood, he had been in the care of Dino "Papa" Golzine, the mafia boss who turned him into the ruthless killer he is now. At first, Ash was just a pretty face for Golzine's pleasure, but now estranged from him, a 17-year-old Ash runs his own gang with an iron fist.

Eiji Okumura is a young Japanese photographer. Traveling to New York as an assistant, Eiji is set to work on a report about kids living in the streets. There, he meets teenage gang leader Ash and is mesmerized by the boy—who in turn is curious about Eiji's different lifestyle.

But this is the dark underground of New York, and recently a series of murders has surfaced in the city, connected only by the words "Banana Fish." With personal stakes in this mysterious battle, it is up to Ash, Eiji and their allies to discover what exactly "Banana Fish" is, where it came from and how to get rid of it—before the world as they know it descends into chaos.