After the success of 1992's Godzilla vs. Mothra, Toho decided to resurrect another classic monster from the Showa era, Mechagodzilla. The original draft of the film featured a Mechagodzilla corrupted by a computer virus that went rogue, turning against its creators and becoming a metallic monstrosity.
After screenwriter Wataru Mimura was brought in and the previous draft was scrapped, a more cohesive and developed version of the film began to form. Mimura was urged by Shogo Tomiyama to include Baby Godzilla in the screenplay to appeal to female fans, who had made up a large amount of the audience for Godzilla vs. Mothra, and also to allow Godzilla to defeat Mechagodzilla in the end.
After Mimura completed his draft of the screenplay, several elements were changed and removed in order to better suit the film's budget and the studio's vision for it. The finished version of the film was released on December 11, 1993.
In order to combat the threat posed to the world by Godzilla, the United Nations forms the United Nations Godzilla Countermeasures Center, a special organization dedicated to defending humanity from Godzilla. The military branch of the U.N.G.C.C., G-Force, constructs the warcraft Garuda and a giant robot built in Godzilla's image: Mechagodzilla. Aside from an impressive array of firepower, this machine features the ability to split apart into two vehicles, an aircraft and a tank.
Meanwhile, when a group of scientists on Adonoa Island recover a perfectly intact prehistoric egg, they are attacked by two pteranodons. G-Force deploys one of the vehicles that form MechaGodzilla to the island, where it kills one pteranodon and knocks the other into the ocean. The egg is brought back to Japan, where it hatches into a juvenile Godzillasaurus, a natural enemy of the pteranodon millions of years ago. Strangely, the two pteranodons on the island had tried to raise the egg as their own child despite it being a member of an enemy species.
In the waters off Adonoa Island, the surviving pteranodon is exposed to radiation and mutates into Rodan, which flies to the Japanese mainland to recover Baby Godzilla. Both Mechagodzilla and the Garuda intercept Rodan, easily killing him before Godzilla arrives, also intent on recovering the infant. Using its immense firepower and transforming capabilities, Mechagodzilla manages to kill Godzilla, but the Garuda is destroyed in the battle. The Garuda explodes, releasing a huge amount of nuclear radiation into the air, which revives Godzilla. Godzilla retaliates and destroys Mechagodzilla, then takes Baby Godzilla with him out to sea, carrying him in his teeth.
- According to Wataru Mimura, Koichi Kawakita decided to have Rodan revive Godzilla instead of the Garuda's explosion in order to better fit with the film's central theme of life against artificial life.
- This film's version of Mechagodzilla's ability to split apart into different vehicles and recombine was later used for Super Mechagodzilla in the finished film and M.O.G.U.E.R.A. in Godzilla vs. SpaceGodzilla.
- In an even earlier version of the screenplay written by Shinji Nishikawa, Godzilla would explode due to an out of control nuclear reaction in his heart during the final battle. The radiation released by Godzilla would be absorbed by Baby Godzilla, mutating him into a new Godzilla, who destroys Mechagodzilla. This basic premise would be utilized for the ending of Godzilla vs. Destoroyah.