At the start of the OVA; Koji Kabuto, Sayaka Yumi, and Dr. Morimori are trying to get back to the Photonic Power Laboratory in Japan as the Mycenae Empire attack the surface. Their plane is intercepted by General Birdler and the Mikelos. The Million Alpha piloted by Lori & Loru is deployed to fight off the Warrior Beasts before it is caught by Birdler, Lori is killed after Birdler crushes her cockpit; Loru survived long enough to activate Million's self-destruct function to destroy Birdler and the Mikelos. Everyone in the plane mourns their deaths, especially Koji for being powerless to stop it.
Around the world, major cities are being attacked by the Mycenae Generals and are being fought by giant robots of the Photon Lab. The Baion Beta is fighting against General Julicaesar near Egypt's Great Pyramid and Sphinx, Daion Gamma against General Draydou near the Great Wall of China, General Hadias against Venus A in Sydney Australia, and Generals Angoras and Scarabeth against the Great Mazinger in New York City.
Koji and co. plane crashes and their pilot is dead. At an army base, Dr. Morimori explains to the base's commander about how the Great General of Darkness appeared during their vacation in Paris and announced how the Empire would regain the surface. He later explains how Juzo Kabuto knew about them in reports and their origins from the island of Bardos and the use of their Mechanical Beasts that were later made into the Warrior Beasts. Understanding the situation, the commander allows them to use a high speed jet to get to Japan. Dr. Morimori however, went to a hidden control room in the facility. The base is later attacked by Archduke Gorgon and General Ligern to assassinate Koji, knowing the dangers of the Mazinkaiser. As the jet prepares to launch, Dr. Morimori launches missiles that destroy the Mammalian Warrior Beasts and Ligern himself. The resulting damage however caused the control room to collapse, leaving Morimori to die and Gorgon had managed to survive.
The battle looks grim for the Photon Lab robots, both Baion and Daion are destroyed by their opponents; Venus A is wrecked but its pilot Jun Hono survives. Great Mazinger is pushed into a corner by its opponents after destroying a lot of the Warrior beasts, throwing its Great Boomerang at them. The attack missed and Great used its Great Typhoon which did not do anything to the Generals. As they mocked the Great, Scarabeth was cut in two and Angoras was badly damaged when the fin returns after being propelled with the Great Typhoon. The Great finished them off with a Breast Burn, however the Great was too badly damaged to move and remained motionless.
Reaching Japan, the pilot had to leave Koji and Sayaka as the jet could not go any further less the craft would be shot down. Koji manages to find a motorcycle but its low on gas, they are given a ride by a female truck driver named Riki. Stopping at a gas station, they refuel the bike and get supplies. Unfortunately, Archduke Gorgon intercept them destroying the motorcycle Sayaka was on rendering her unconscious. Just as Gorgon was about to kill Koji who went to check on Sayaka, Koji shoots at him with his Photon Gun hitting both of his brains in the tiger and humanoid body. Somehow, he was still functioning but Boss Borot arrives to save Koji. Boss grabs hold of him on a giant chain and repeatedly slam him on the pavement until finally throwing him into the gas station where he is consumed in an explosion. Sayaka is given to Riki to look after as Boss Borot takes Koji to what's left of the Photon Lab.
Koji, thought that the Mazinkaiser was destroyed, but Boss assures him that it's fine. Kaiser was being retrofitted in a satellite above them. Boss reveals that the Kaiser Pilder is in fact inside Boss Borot. The remaining Generals and Warrior Beasts, lead by Dante, arrive to kill Koji. Boss Borot manages to distract them long enough for to give Koji a ride out on the Kaiser Pilder. Boss Borot is then cut into pieces by Dante. The Mazinkaiser is dropped from its containment and goes into the atmosphere. Koji docks into the Kaiser in midair, falling back down to the Earth. As the Generals and Warrior Beasts stare at the smoke, the Kaiser emerges destroying the Warrior Beasts and fights against the Generals, easily defeating them. As Draydou attempts to flee, the Kaiser gives chase with the Kaiser Scrander, and attacks him with the Fire Blaster. Draydou is barely alive and is crushed by the Demonika controlled by the Great General himself.
The craft crashes the Kaiser into Mt. Fuji; but the robot manages to grab, throw, and destroy it with the Kaiser Scrander. The Kaiser faces off against the Great General with its Kaiser Blades. They are evenly matched but the General manages to pin the Kaiser down until it uses Rocket Punches to disarm him. Koji shouts in vengeance the people who were hurt or killed because of the Great General and the Empire, knocking the General into a crater before he is impaled by his own sword.
After the battle, a ceremony is held for Lori, Loru, and Dr. Morimori. Repairs to the lab and Mt. Fuji are going through and the Kaiser picks up the Great Mazinger with Tetsuya and Jun.
- Several characters from Go Nagai's previous works have appeared in a few scenes (e.g. Riki originally came from different manga by Go Nagai like Dororon Enma-kun and Violence Jack).
- An animated version of Nagai himself appeared for a short while drawing the Great General of Darkness with the Grendizer in the background.
- Contrary to popular belief, this OVA is not a sequel of the previous Mazinkaiser OVA episodes. It is actually a stand-alone spin-off of Mazinger Z vs. Great General of Darkness.