A scientist by the name of Shiragami is driven insane due to the death of his only daughter Erica. At the brink of madness, the scientist begins to experiment with biotechnology and is able to successfully combine the DNA of a fish with that of a mammal to create Deutalios, a 50 meter creature that resembles a rat. It's not long after its creation that the beast is found terrorizing Yokohama, attracting the attention of Godzilla who arrives to confront the monster. The two titans engage in combat, but Godzilla quickly gains the upper hand on his smaller opponent and kills the creature. With his foe dead, Godzilla begins to eat the remains of Deutalios.

Meanwhile, Doctor Shiragami continues with his experiments, this time managing to create a hideous creation that he dubs Biollante. However, a female reporter, who is trying to discover the origin behind Deutalios, winds up near Shiragami's lab before she starts to have a physic vision of a group of humanoid flowers chanting her name. The reporter then meets with Shiragami where she relates her vision, prompting the doctor to confess that he had been tampering with the DNA of a tropical plant and that of his deceased daughter, which is what lead to the birth of Biollante.

Eventually, Godzilla appears again and Biollante leaves the vicinity by burrowing underground toward the nuclear leviathan, emerging next to its opponent. Biollante uses its radioactive sap spray on the King of the Monsters, which badly burns Godzilla and forces him to retreat into the sea. Shortly afterwards, though, Biollante is consumed by a cloud of smoke as her mutation goes out of control.

This was the original script for the film Godzilla vs. Biollante (1989). Reportedly, Toho held a story contest in 1986 for the next installment of the Heisei series, tentaveily dubbed Godzilla 2, and the winner was Shinichiro Kobayashi, a dentist, who created this early draft for Godzilla vs. Biollante. The original story was very different from what would evolve into Kazuki Omori's final script though. What little did survive includes: the death of Erica, her father being the creator of Biollante through her DNA, a psychic girl and, for the most part, the climax.

After going over the winning entry, producer Tomoyuki Tanaka and Omori felt that Godzilla was not focused on enough in the story. So the concept was changed heavily to focus instead on Godzilla rampaging across Japan for a majority of the movie. Elements from another script in the contest, which involved utilizing Godzilla's cells, where also incorporated as it became an important subplot to the movie as the Self Defense Force now had the objective of creating and utilizing the ANEB. It was also decided that the Super-X concept would be continued for the feature, as a second version of the craft would appear.

Omori's new vision for the production also called for the axing of the Deutalios creature, and instead creating a earlier form of Biollante that closely resembled a rose in its place. The psychic elements hinted at in Kobayashi's initial concept were also focused on much more in the final screen play, as the movie would introduce the character Miki Saegusa and her school of "gifted" pupils. Interestingly to note, in Omori's original screenplay, Miki was intended to lift Godzilla, using telekinesis, during their confrontation; however, this idea was removed as Tanaka was extremely opposed to the concept.