After the first season, Afro is trying to live an ordinary life, but is hated by many because of his past. One stormy night Kuma and Sio attack Afro, take his Number One headband and his father's remains. Sio tells Afro her plans to resurrect his father so she can torture him. Afro decides to find the Number Two headband , as only the Number Two can defeat the Number One. Sio wants revenge for the lives destroyed because of his quest for revenge. She also blames Afro for what has happened to Jinno (Kuma) who, during a flashback, is revealed to be her older brother. After getting his sword sharpened and cleaned, Afro stops at a gambling house run by Brother 3 of the Empty Seven Clan, of which he and Brother 1 (now paralyzed, bound to a stretcher, gibbering nonsense) are the only survivors . He challenges Afro to a game of dice. If Afro wins, he will get the information on the headband, but will lose his head if he doesn't. Brother 3 tries to cheat using loaded dice, but Afro uncovers the ruse. Beaten, Brother tells him the name and location of the current wielder: Shichigoro.

Afro sets out and soon meets the man, coincidentally, as he is trying to save his son, Kitaro, from a bandit. The two get to know each other and develop a silent respect. However, Shichigoro knows what Afro is after but won’t relinquish the headband without a fight (mostly due to a promise he made to Kitaro’s real father to stop the killing by hiding the headband). The two battle; Afro, trying not to kill Shichigoro, is forced to take the fight into crowded areas to gain an advantage,. Both are hindered by Sio's henchmen, who try to get the drop on them; but they are quickly dispatched. In the end, Afro manages to win by stabbing Shichigoro through the body of one of Sio's henchmen, much to the horror of a watching Kitaro.

Sio and Jinno confront Afro and inform him to meet them at Cherry Hill for the final battle, and show Afro the living spine and head of his father. Soon Afro reaches said spot but first must contend with cyborg versions of Sio's family that were indirectly murdered because of Afro. He’s wounded badly, but defeats them in a massive battle. During the battle Sio murders Dharman and releases Afro's father prematurely. Afro arrives at the final spot, where Sio and Jinno await. Rather than fight Afro themselves, they reveal his father‘s clone, a psychopathic brute because his development was stopped prematurely. Afro goes into shock as the clone attacks him. Ninja-Ninja tries to convince Afro that the clone isn't his father. But Afro is hesitant , beaten senselessly, and then strangled to death. Seeing Afro dying Sio starts to relish her successful revenge, but positive memories from Afro and Jinno’s training are triggered in Jinno. Afro's suffering brings back Jinno's lost personality, and he refers to his duty to 'protect the dojo' and his 'brother' Afro. Jinno attacks the clone but is outmatched, being cut in half by the clone. Sio attempts to save Jinno, but is impaled by the clone's sword. As both die in each others' arms, Jinno says "It's been a while, hasn't it Sio?". As Sio dies, her expression is that of contentment. As the clone takes the Number One headband, an electrical current from Jinno's body is conducted along their blood onto Afro, resuscitating him..

Realizing his father is dead, Afro takes Jinno’s sword, wrapping the Number Two headband around his hand. After one last standoff, Afro kills the clone, taking back his headband. As he heads back to Mount Shumi with Ninja Ninja, Kitaro, who had been following Afro, confronts him with Shichigoro's sword. Afro gives him the Number Two headband, telling him, "Anytime you're ready,". At the end, a scene shows Takimoto, a masked ninja, waiting in a wasteland (most likely the number one's throne room due to the background). Noting someone approaching, he says "Been waiting a long time for you". The person in question being none other than Justice.