When King Ghidorah suddenly attacks Osaka, the military deploys the Super X II to locate Godzilla, and they use a transmitter to control the mutant dinosaur. Godzilla is led to Osaka, where he fights and kills King Ghidorah. Immediately afterwards, Ghidorah's body vanishes and an alien spaceship appears. The invaders reveal that they were controlling Ghidorah, and demand that the human race surrender. Meanwhile, another Godzilla appears in Mt. Fuji, and the Super X II lures the real Godzilla there to fight it. Godzilla confronts the new Godzilla, who is revealed to be Mechagodzilla wearing an artificial skin. During Godzilla's fight with the robot, the aliens kidnap Dr. Shiragami and take him to Lake Ashino. Godzilla goes there to rescue the professor, and is confronted by Biollante, his plant-like clone. After defeating Biollante, the Super X II rescues Shiragami, it is revealed that the doctor had recovered DNA samples of Godzilla and King Ghidorah and had been experimenting on them to create a serum that enhances the physical attributes of any being. However, the aliens invaded his laboratory and stole the samples, using them to create Biollante.