A reporter, Ichiro Sakai, and two scientists stumble upon Godzilla's unconscious body, which washed ashore during a storm. The creature is presumed dead, and goes under the interest of a businessman who wants to commercially exploit the carcase as a tourist attraction. Eventually, though, Godzilla awakes and commences to terrorize humanity once more. The nuclear menace makes his was toward Rolisica, who try and rebel the monster using Frontier Missiles, but to no avail. Ichiro and the two scientists end up venturing to Infant Island in order to ask for Mothra's aid in defeating Godzilla. In return for Mothra's help, the three offer themselves up as hostages. The natives agree and Mothra flies off to confront Godzilla.

Meanwhile, after trampling Himeji Castle, Godzilla moves east toward Tokyo, where the Japanese Self Defense Force has set up Artificial Lightning Generators. The towers attack Godzilla, but unfortunately the creature gains an immunity to the attack and moves onward toward the beach where he finds Ichiro and the two scientists. Fortunately, Mothra arrives on the scene just in time to save them, and attacks Godzilla head on in a final confrontation.

There were several differences in the original screenplay from Shinichi Sekizawa, which he submitted in 1963 on December 31st, compared to the finished product. The most noticeable is that Godzilla's body was substituted for Mothra's Egg in the final draft. Furthermore, Godzilla was also going to take a bigger role in the film, with Mothra only arriving just in time for the climax. Rolisica, a fictional land that was featured in Mothra (1961), was present in this early screenplay as well. The Rolisican government was also going to be the ones to deploy the Frontier Missiles against Godzilla, as opposed to the US forces as it occurred in the International version of Mothra vs. Godzilla (1964). Lastly, this early draft didn't feature Mothra's Larva at all, and the final confrontation was going to be with the Imago version of Mothra and Godzilla.