The story begins in a ruined world where humanity has been wiped out by the Mazinger Z turned evil and Koji is the only human remaining. An android approaches him and offers Koji a chance to stop the carnage, he accepts and the android uses Rust Hurricane to destroy his body. The android, Minerva X does so to send his soul back to the past.
This was not the first time however and several attempts to stop Z from becoming a literal 'Majin' (Demon God) have ended in failure and the repetition of everything in existence being reduced to nothing (or reduced to 'Zero' as the characters say). One attempt however brought Koji to a world where he is currently piloting Z with Sayaka aiding him in battle and his brother Shiro is still alive. Minerva had been brought into creation by that world's Dr. Hell, but she abandons him and joins Koji and his allies in the coming battles against Hell.
A few days later, Koji reveals to everyone about Minerva and they don't mind. Enjoying her new life, Minerva discovers that prior to her arrival was the Mazin War. Dr. Hell had already conquered nearly the entire world with his Mechanical Beasts and Bardos Wand that allowed him to overpower every government power and weapon in the world. Japan was the only area exempt due to Mazinger Z that Koji received from his grandfather who was not as mad as his other counterparts. 5 billion people were killed in the attack worldwide as a result after being robbed of their dignity and humanity. The Mazinger Army was then sent to fight them and after a long battle the pilots of the captains of the army had died in action, Sayaka survived but her robot Venus A was destroyed, and Koji is gravely wounded and his body is dead after fighting in a duel against Dr. Hell. Koji is brought back to life as a cyborg with a special Airborne Element Fixing Device. In order to prevent further casualties a Photon Barrier with a 200 km radius is put up around Japan's Kanto region.
Minerva is astonished by this but is relieved to see Mazinger Z as a symbol of hope. Minerva remains determined not only to keep Mazinger from turning into a Majin but also stop Dr. Hell without the transformation. Dr. Hell however sends a barrage of Mechanical Beasts at the Photon Barrier to break through. Mazinger and allies manage to fight off most of the Mechanical Beasts but the barrier falls because of a suicide mission by Count Brocken. The flying island of Bardos then reveals itself as the gigantic Mechanical Beast Gordon Hell and challenges Mazinger Z to a final battle.
In battle, Mazinger is damaged but Minerva integrates with Mazinger to patch up the robot and buy time to repair the barrier. When Koji and everyone are safe, Minerva reveals the truth about the world's annihilation that had repeated time and again. With Mazinger given emergency repairs, Koji mobilizes Z to fight Hell King Gordon but the robot's massive size and power forces Mazinger Z to unleash some of the Majin Power boxes installed into it allowing it to access more power and attacks. Koji however was almost consumed by the raw power until Minerva interrogated him through the connection with Mazinger Z allowing Koji to keep his sanity.
Up until the sixth black box of Majin Power, Mazinger fights back but in order not to activate the seventh black box Koji hesitates which gets him and Mazinger caught in a whirlwind. Sayaka in the Artemis A comes to the rescue renewing Koji's hope and determination to fight until the very end. However, the situation still looks hopeless as the Gordon overpowers Mazinger at nearly everything. However reacting to the Z are the Mazinger Z and Koji Kabuto's of each past reality. The combined power of the Mazinger Z's throughout time and space counter and overpower the Gordon. The hopes and strong feelings of all of Koji's comrades also fills the Mazinger with great power and with the combined power of all, Mazinger Z unleashes the Breast Fire Dynamic Fire Nova attack obliterating the Hell King Gordon and Dr. Hell. Peace is restored and Mazinger manages to avoid the tragic fate that awakened the Majin Change.
Unfortunately, the epilogue shows Dr. Morimori and other scientists being killed off by Archduke Gorgon who survived the battle and a prophet appearing stating that the end of the world is coming near.