The manga begins with the Mazinger Z and Great Mazinger fighting against an alien machine after the Diana A and Venus A have been taken down. In the meantime, the Saotome Institute pilots want to help out but are unable to as their robot is not complete yet. Michiru Saotome uses her Lady Command jet to get Sayaka Yumi and Jun Hono away from the battle. Professor Yumi sends to Great Booster to get Koji and Tetsuya to retreat. However Tetsuya's injuries make him unable to move. To buy Tetsuya time, Koji has Mazinger Z take the Mazinger Blade and distract Pikardon. While Great is moved away from the battlefield, Z sees the robot change into Pikadron with its claw stabbing through its body, electrocuting the robot, and throwing it into the ocean.
After the battle, the Pikadron robots reduce Tokyo to ruins. The Getter team explain their own encounter with Pikadron which at the end of the battle killed their friend Musashi Tomoe. As they go to see Tetsuya Boss lashes out on them for not helping them. As he and Benkei Kurama argue they are stopped by Jun and Tetsuya who inform them that now is not the time to argue.
Mazinger Z had been recovered, but Koji was nowhere to be found and presumed to be dead to Shiro and Sayaka's sadness. Professor Yumi informs them to mourn Koji later as he and Prof. Saotome are coming up with a counterattack to Pikadron. As the Getter team go back to Mt. Asama, Ryoma asks Hayato what Prof. Yumi and Saotome are working on. Hayato replies that it is a method to combine Photonic and Getter Ray Energy. As Pikadron's soldiers approach, the Getter team manages to avoid them with clever maneuvers.
However, they notice that the robots are going for the Saotome Institute as the Getter robots are as big a threat as the Mazingers. To fight against the threat coming their way, the Getter Team decides to mobilize the Shin Getter Robo. After disabling the guards and workers they fly the mecha out to fight the robots. The Shin Getter succeeds in destroying the robots but with the way it was launched, it will take time for it to fly again.
Prof. Saotome and Yumi make the finishing touches on the robot and the power combiner. To stabilize the energy, the new robot uses the Photon engines of Z and Great. Michiru, Tetsuya, and Jun come to tell Prof. Saotome that the Getter Team had launched the Shin Getter but are astonished by the new robot before her eyes.
In Tokyo, the Shin Getter Robo had entered its Getter 2 form and fends off Pikadron's robot army. But suddenly a large egg appears from the ground and is hit from a beam in the sky. The egg hatches and reveals Gilgilgan with four heads. The creators of the monsters, the Damdom appear and have Gilgilgan eat the Pikadron robots. To combat this new threat, the Shin Getter enters its Getter 3 state. Unfortunately, the missiles it fired are devoured by Gilgilgan who grows a humanoid body out of its back that attacks the Getter with a beam from its mouth. The Getter manages to separate in time and renter its Getter 1 state but immediately loses energy and crashes to the ground about to be devoured by Gilgilgan.
Fortunately, the Double Spazer appears with a still living Koji firing its Cyclone Beam to distract Gilgilgan. Hikaru Makiba had rescued Koji with the Marine Spazer and brought him to the Space Science Laboratory to pilot the Double Spazer. Boss and Michiru tell Koji to get back to the Photon Lab as there is a new Mazinger robot ready to mobilize. Koji does so and after a warm welcome is introduced to the super robot Mazinkaiser. The robot is powered by both Photonic and Getter Energy using a reactor from the cores of Z and Great giving it unlimited power. Tetsuya tells Koji to fight in his place while Sayaka gives him his old pilot suit thinking that the suit he was wearing wasn't much of a fashion statement. Suited up, Koji departs on Mazinkaiser.
The battle with Gilgilgan isn't going well with the bottom half of Boss Borot being bitten off and the Shin Getter barely able to save it. As they are about to be attacked by Gilgilgan and the Pikadron robots, the Kaiser arrives using the Scrander Boomerang to cut through some of Gilgilgan's heads and the robots. It later shows off more of its attacks destroying the rest of the crowd. Kaiser also allows the Shin Getter to restore energy with its system.
However, the battle wasn't over, Gilgilgan separated from its old body to become Mecha Gilgilgan. The super robots tried to fight off Gilgilgan but the monster was impervious to their attacks and could actually absorb the metal from their bodies and equipment. So the robots stick to beam attacks which Gilgilgan can't absorb. But even with this new weakness found, the monster reveals that it can regurgitate eggs that when hatched could lead to another monster like Gilgilgan.
Tetsuya then notices that while it is absorbing the Getter Tomahawk, it is unable to absorb the Super Alloy New Z alpha of Mazinkaiser's fist and informs Koji. Koji then goes in for a frontal attack with Kaiser. As Gilgilgan tries to attack Kaiser, Shin Getter blasts its weapons.The Kaiser then makes a hole in Gilgilgan with the Kaiser Scrander before letting go and performing a combo attack with the Shin Getter. The Kaiser unleashes its Fire Blaster while the Shin Getter uses its Getter Beam, the colliding attacks in the hole. While Boss Borot watches, he is dropped off the Lady Command and onto the Damdom ship causing it to crash into the beam collision destroying it and Gilgilgan. The explosion caught all of the eggs burning them. While victorious, the battle was far from over, the threat of the Damdom still linger but the heroes are confident that the Kaiser and Shin Getter can protect them from threats.