In The Return of Godzilla, the famous monster is re-invented to be taller and more powerful, at 80 meters tall and 50,000 metric tons. Return of Godzilla ignored all previous films in the series aside from the original. This second Godzilla was the product of a botched time travelling mission, which involved travelling back to 1944 and transporting an injured Godzillasaurus residing on Lagos island to the Bering sea, thus preventing its exposure to the H-bombs.

The Godzillasaurus lay dormant in the Bering sea till the late 1970's, where it was exposed to radiation after a nuclear sub accident. Hungry for nuclear energy, the new Godzilla attacked a Russian nuclear submarine before turning towards Japan's nuclear powerplants. After his battle with the Super X, Godzilla was lured to Mount Mihara by Professor Hayashida, where he would be dropped into the lava below. There he entered a state of dormancy.

During his slumber, Japan developed an underfunded counterance agency, designed to track any and all of Godzilla's future sightings in Japan. Anti-Nuclear Energy Bacteria (ANEB) was also developed by Japanese corporations in order to provide the country with a counter to nuclear accidents or attacks.

Reawakened by explosions detonated during a botched terrorist ransoming, Godzilla headed for Lake Ashino where he would do battle with Biollante in Godzilla vs. Biollante, the hybrid monster of Godzilla’s own DNA and the cells of a rose that had bonded with the soul of a scientist's daughter. After their first batttle was done, Godzilla was confronted by a new Super X-2 that distracted the monster so soldiers could administer the ANB through rocket propelled grenades.

Super X-2 was badly damaged during the battle, unable to further engage Godzilla. In an attempt to activate the ANEB, Godzilla was lured to a site with experimental lightning generators whose purpose would be to increase Godzilla's core temperature so the bacteria could function properly. At the site, a new form of Biollante arrived and besieged the weakening Godzilla.

The ANEB had taken effect and forced the battle to draw. Biollante was mortally wounded and Godzilla had fallen into the ocean, where he would die from the ANEB. The cold waters of the Pacific would lower Godzilla’s body temperature, forcing the ANEB to denature and allowing Godzilla to live on.