Beginning moments after the events of "Godzilla 1985," we are shown Tokyo in its state of destruction after Godzilla's attack. Godzilla had been lured into the crevice of a volcano by solar noises and teams have begun repairing the city. In the rubble, a radiation containment team discover pieces of Godzilla's flesh lying among the ruins. Upon picking up samples, the group is mercilessly gunned down by a team of mercenaries who take the samples of Godzilla's DNA. A sunglasses-wearing agent kills the escaping unit and takes the briefcase with Godzilla's samples within. The Saradian Oil company then employ Dr. Shiragami to convert their desert country into farmland which they plan to use Godzilla's reproducing cells for. However, a terrorist group breaks in, destroying the remaining cells and killing Shiragami's daughter Erika in the bombing.5 years later, Shiragami has returned to Japan and merged Erika's remaining cells into that of a large rose bush in an attempt to preserve her soul. Other members of the department have been collecting the cells in order to make a weapon should Godzilla escape from his volcanic grave. Their weapon is dubbed "Anti-Nuclear Energy bacteria." They approach Shiragami to help supervise the project with some remaining of Godzilla's cells, but he refuses. Soon after, the volcano begins erupting and Godzilla begins slowly emerging from the fiery chasm. Since the anti-nuclear weapon is not finished yet, the Japanese Government sends their only available weapon, the newly improved Super-X 2 to fight Godzilla. The main weapon within it is the reflective mechanism that can reflect Godzilla's flaming breath upon him should he attack it.Meanwhile in Shiragami's lab, several terrorists break in to try and steal his research but are attacked by the agent wearing dark sunglasses who is revealed to have been working with the Saradian company all along. Suddenly in the firefight that breaks out between them, the mutated rose bush Shiragami has been working on comes alive and kills some of the fighters. The next morning, a gigantic rose-like mutation is seen protruding from the harbor. Shiragami observes this and dubs it the name "Biolante." The Biotech company threatens to detonate missiles at the volcanic crater and free Godzilla should they not receive the anti-nuclear material. During the trade, the Saradian agent attacks and steals the material before setting off the missiles which detonate and free Godzilla. He roars angrily and begins his terrorizing trek towards the city. As he does so, Biolante comes alive and begins screeching.Godzilla is chased into the harbor where he is attacked by Japan's air-force and navy. However, despite the heavy missiles and artillery fired upon him, Godzilla fights back and destroys many naval vessels and jets, reducing their attempts to stop him into rubble. The Super X 2 is sent out to battle Godzilla. This unmanned aircraft reflects Godzilla's fire upon himself but does not seem to hurt him. He instead manages to damage the Super X 2's fire mirror, forcing it to turn back. Biolante begins mutating and grows teeth. Shiragami begins to fear that it is no longer his daughter's soul within the plant, but Godzilla's violent influence. Godzilla approaches Biolante and the two begin battling with Godzilla becoming bound within its tentacle-like vines. Shiragami oversees this and deduces that both Biolante and Godzilla are the same thing and that only one of them must remain on this earth, hence the battle to destroy each other. Godzilla breathes back with his flaming breath and destroys Biolante, only for Biolante to regenerate until it retreats.Godzilla begins marching towards a nuclear power plant in Osaka to regenerate his power having been drained from his battle with Biolante. Godzilla begins his rampage on Osaka and is attacked by Super X 2, having been repaired, but Godzilla easily destroys it. He is then shot with several bazookas with the Anti-nuclear substance within. Despite being hit, he does not seem to be hurt since the weapon within him is only triggered when is hot. He kills the men who shot him and the government begins trying to find a way top make his body temperature rise. Biolante regenerates and takes the form of a hideous doppelganger resembling Godzilla. Biolante and Godzilla engage in a brutal battle with Biolante projectile vomiting upon Godzilla, urging his temperature to rise putting the anti-nuclear weapon within him to take effect. Godzilla collapses on the shore. Despite speculation of collecting Godzilla's cells for research, Dr. Shiragami refuses to do so, saying he has learned his lesson from Biolante's existence. He then muses that scientists like him are the only real monsters in their creations of such abominations.Having defeated Godzilla, Biolante disintegrates into the heavens and Shiragami sees the soul of his daughter finally freed from the creature he created. Upon viewing this in wonderment, Shiragami is shot in the back by the Saradian agent. The agent attempts to escape but rushes upon a radiation plate and is incinerated by lightning. Godzilla awakens, the ocean water he collapsed into having cooled his body temperature. Instead of attacking the city, Godzilla observes the people gathered nearby and then turns around and swims off into the ocean. Dr. Shiragami dies of his wound and is finally at peace.