Afro has found peace and tries to live an ordinary life, but is still hated by many because of his killing, and also is still attacked by those who want his headband. One stormy night Kuma and Sio attack Afro, take his Number One headband and his father's remains. Sio then tells Afro her plans to resurrect his dead father so she can torture him. Upon hearing this, Afro decides to find and reclaim the Number Two headband once more, as only the Number Two can defeat the Number One. Sio wants revenge on Afro for the people he has killed on his journey to become the Number One. She also blames Afro for what has happened to Jinno (Kuma) who, during Sio's flashback, is revealed to be Sio's older brother. After getting his sword sharpened and cleaned, Afro first stops at a gambling house run by Brother 3 of the Empty Seven Clan, of which only Brother 1 (now paralyzed and bound to a stretcher, mostly gibbering nonsense) and he are the only survivors after the events of the first series (along with the mysterious Brother 7 who has yet to appear). He challenges Afro to a game of dice. If Afro wins, he will get the information on the Number Two headband. If Afro loses, Brother 3 takes his head. Brother 3, however, tries to cheat using loaded dice, but Afro quickly uncovers the ruse. Beaten at his own game, Brother 3 gives up the information that a man named Shichigoro has it and where to find him.
Afro sets out and soon meets up with the man, coincidentally, as he is trying to save his son from a bandit. The two eventually get to know each other and gain each other's silent respect. However, Shichigoro knows what Afro is after but is unwilling to relinquish the headband without a fight (moreover due to a promise he made to his son's real father). Thus the two do battle; Afro, while trying not to kill Shichigoro, is forced to take the fight into crowded areas to gain the advantage, though both combatants are hindered somewhat by Sio's henchmen, who try to get the drop on the two but 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 Shichigoro's son, Kitaro, who witnessed the end of the battle. Regardless Afro continues on, the Number Two headband regained.
Sio and Jinno soon met up with Afro and inform him to meet them at Cherry Hill for the final battle, showing Afro the spine and head of his father to get him riled. Soon Afro reaches said spot but first must contend with cyborg versions of Sio's family that were indirectly murdered by Afro. He is wounded badly, but manages to beat them after a massive battle. During this battle Sio murders Dharma and releases Afro's father prematurely. A weary and bloodied Afro continues to the final spot where Sio and Jinno are waiting. But rather than fight Afro themselves, they reveal the revived form of Afro's father, Rokutaro (albeit now more of a psychopathic brute as Sio stopped the resurrection development before reason could be added to the clone). This causes Afro to go into shock as the clone attacks him. Throughout the fight, Ninja-Ninja tries convince Afro that the clone isn't his real father. But Afro is hesitant to attack, thus he is beaten senselessly by his clone father and eventually strangled to death. Seeing Afro in his dying moments, Sio starts to relish her successful revenge, but positive memories of comradeship (when Afro and Jinno were still in training) are triggered in Jinno. Afro's suffering brings back Jinno's lost personality, and in spite of Afro's violent past, Jinno forgives him, referring to his own duty to 'protect the swordmaster's dojo' and calling Afro his 'brother'. Jinno then attacks the clone but is not powerful enough to defeat him, and is cut in half by the clone. Sio attempts to save Jinno, only to be impaled by the clone's sword. As both die in each others' arms, Jinno says "It's been a while, hasn't it Sio?", which refers to the period when he acted only like an emotionless cyborg and was unable to speak or act like a real brother towards her. This shows Jinno has regained his sanity, and can finally die in peace. As Sio dies, her expression is that of contentment in her knowledge that her brother is back. This probably suggests that all she actually wanted was the return of her brother, and her rage towards Afro was fueled by her helplessness to bring him back. As the clone takes the Number One headband for himself, an electrical current from Jinno's body is conducted along their blood onto Afro, bringing him back to life.
Finally coming to terms that his real father died a long time ago, Afro takes the sword of his fallen friend, wrapping the Number Two headband around his hand. After one last standoff, Afro is able to kill his father's clone and take back the Number One headband. As he heads back, Kitaro, who had been following Afro much of the way, confronts him with Shichigoro's sword. Afro gives him the Number Two headband and tells him, "Anytime you're ready," just as Justice had told him as a boy. With that, Afro, along with Ninja-Ninja, head back to their home on Mount Shumi. At the end credits, a scene shows Takimoto, a masked ninja, waiting patiently in a wasteland (most likely the number one's throne room due to the background). Noting someone approaching, he mentions "Been waiting a long time for you". The person in question being none other than Justice as the movie closes
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