The Heisei films are set in a single timeline, with each film providing continuity to the other films, and brings Godzilla back as a destructive force of nature that is feared by humans. The biological nature and science behind Godzilla became a much more discussed issue in the films, showing the increased focus on the moral aspects of genetics.
The Japanese fishing vessel ''Yahata-Maru'' is caught in strong currents off the shores of Daikoku Island. As the boat drifts into shore, the island begins to erupt, and a giant monster lifts itself out of the volcano. A few days later, reporter Goro Maki is sailing in the area and finds the vessel intact but deserted. As he explores the vessel, he finds all the crew dead except for one young man called Hiroshi Okumura, who has been badly wounded. Suddenly a giant ''Shockirus'' sea louse attacks him but he is saved by Okumura.
In the aftermath of The Return of Godzilla, the monster's cells are delivered to the Saradia Institute of Technology and Science, where they are to be merged with genetically modified plants in the hope of transforming Saradia's deserts into fertile land and ending the country's economic dependence on oil wells. Dr. Genshiro Shiragami and his daughter, Erika, are enlisted to aid with the project. However, a terrorist bombing destroys the institute's laboratory, ruining the cells and killing Erika.
In 1992, science fiction writer Kenichiro Terasawa (Kosuke Toyohara) is writing a book about Godzilla and learns of a group of Japanese soldiers stationed on Lagos Island during the Gilbert and Marshall Islands campaign. In February 1944, while threatened by American soldiers, the Japanese soldiers were saved by a mysterious dinosaur. He theorizes that the dinosaur was subsequently mutated into Godzilla in 1954 after a Castle Bravo on the island. Yasuaki Shindo (Yoshio Tsuchiya), a wealthy businessman who commanded the Japanese soldiers on Lagos Island, confirms that the dinosaur did indeed exist.
Japan is caught in the middle of a three-way battle between Godzilla, the divine Mothra, and her dark counterpart Battra.
In 1992, the United Nations establishes the United Nations Godzilla Countermeasures Center (UNGCC) to stop Godzilla. The mechanical middle head of King Ghidorah is salvaged by the UNGCC's military branch, known as G-Force, and Reverse engineering to create two anti-Godzilla machines, the first being an aerial gunship called Garuda and a mecha modeled after Godzilla called Mechagodzilla.
Godzilla cells brought into space by Biollante and Mothra are exposed to intense radiation from a black hole, resulting in the birth of "SpaceGodzilla", which quickly makes his way to Earth, destroying a NASA space station along the way.
Miki Saegusa of the United Nations Godzilla Countermeasures Center (UNGCC) travels to Birth Island to check on Godzilla and his adopted child Godzilla Junior, but finds the entire island destroyed. Godzilla appears in Hong Kong, covered in glowing lava-like rashes, and goes on a rampage. The Japan Self Defense Forces (JSDF) hires college student Kenkichi Yamane, the grandson of Dr. Kyohei Yamane, to work at the center in an attempt to unravel the mystery of Godzilla's condition. Yamane suspects that Godzilla's heart, which acts as a nuclear reactor, is undergoing a nuclear meltdown as a result of Godzilla absorbing the energy released from a uranium deposit on Birth Island that had been triggered by a volcanic eruption. Yamane theorizes that when Godzilla's temperature reaches 1,200 °C, he will explode with a force approximately "1,000 times greater than all nuclear weapons put together, a burst of power unseen since time began," which will be hot enough to ignite Earth's atmosphere and reduce the planet's surface to ash.