In a futuristic yet feudal Japan, it is said that the one who wields the Number 1 headband is the strongest fighter in the world and shall possess godlike powers. The only way to obtain the Number 1 headband is to challenge and defeat him in combat. However, only the Number 2 can challenge the Number 1, while anyone can challenge the Number 2 which causes a constant struggle for the Number 2 headband.
Justice, the owner of the No. 2 headband, goes to fight the owner of the No. 1 headband, Rokutaro. The two battle, ending with Justice decapitating Rokutaro and claiming his headband. Rokutaro's head rolls in front of his son, a young boy named Afro, as he sobs and vows revenge.
Now an adult, Afro Samurai is the current No. 2 and a master swordsman. He travels Japan trying to make his way to the mountain-top keep where Justice awaits. As he makes his way to Justice, he recalls his journey from a frightened young boy to a master samurai. Along the way, many people challenge Afro for his headband, including the "Empty Seven Clan" who send various agents, including a robotic Afro, to kill him throughout his travels. He is also being hunted by his vengeful childhood friend Jinno, who was long thought to be dead. Afro eventually defeats his enemies, Jinno, and confronts Justice, whom he defeats and takes the No. 1 headband from.
Afro decides to live in the mountains once again, when Jinno, adorned with every headband in existence, confronts Afro for the No. 1 band and his revenge.