Afro Samurai, a black samurai, seeks revenge from a man named Justice who killed his father and happens to be the #1 fighter in the world. After Afro earns the rank of #2 fighter needed to challenge #1, he starts his lonely walk to revenge. He faces bounty hunters, bar thugs and fanatical monks - all who seem to have clues to the whereabouts of Justice and all of whom covet the title of #2 for themselves.

Bloody, broken and near death, Afro awakes under the care of a mysterious and beautiful woman named Okiku. As she heals him, he dreams of his younger days as an orphan, saved from thugs, and trained among other orphans in a secret sword school led by a wise sword master. Still bent on revenge, he is a dark and quiet boy with few friends.

Afro's climb of Mt. Shumi is blocked by the fanatical Empty Seven; after attacking him, they unleash Afro's most lethal opponent yet: himself.