After defeating a group of robots in battle at an abandoned amusement park, a human resistance fighter slips inside Castle Promise, a massive robot-manufacturing facility. Luna Kozuki plans a revolt with the human workers; that night she sees Lucky and her old lover, Tetsuya Azuma. The next day, the rebels are betrayed by a fellow prisoner who was promised freedom; the collaborator is killed and Luna is captured. Akubon plans to publicly execute her as if she were Casshan, to break the people's spirit. However, the real Casshan saves Luna and kills Akubon, though the Black King escapes.

Luna leaves to deliver weapon plans to Admiral Rudolph, the leader of the human forces. Her helicopter is shot down and crashes, and the pilot sacrifices himself to allow Luna to escape a robot scout team. Luna is able to meet with Casshan and Friender, and finds that Casshan is struggling with his lack of humanity while also suffering physical weakness from the battles. The three are attacked by a robot army and Casshan tells Luna to flee but she is unable to leave Casshan.

The Black King has a bridge repaired, while the human resistance plans to bomb the bridge when the enemy forces cross it. Meanwhile, Casshan and Luna are ambushed by robot scouts, which Casshan and Friender defeat; Casshan hacks into a scout and learns the Black King is initiating the Sigma Project to replace humans with Eco-friendly androids. While struggling with what to do, Casshan's mother appears to him and tells him to stop the Black King. Luna meets up with the resistance and Casshan stops them as the train crosses the bridge, but immediately regrets it. The bomb explodes too late, but Casshan redeems himself by destroying the train and vows to never again lose his way.

Using the weapon plans, the human resistance make a large number of MF guns and attack the robot army. Victory seems at hand but Casshan's mother warns that the Black King is biding his time. Luna tries to comfort Casshan who rebuffs her, and leaves with Friender to battle the Black King. The Black King launches his offensive and gains control of the world's nuclear missiles. Friender sacrifices himself during a battle and Casshan is shot by a female robot commander who realizes he was more than human or machine. Casshan fights the Black King and after the Black King claims to possess his father's soul - gathers enough strength to kill the Black King, dying himself afterwards. A fail-safe shuts down all the other robots, securing human victory and a future for Luna.