While scouring the sewers of New York, Nick Tatopoulos discovers one of Godzilla's eggs has survived. The hatchling that emerges escapes and by the time the team find it again, has grown to a massive (but thankfully harmless) sub-adult. As the team try to study the new Godzilla, the U.S. military, responding to a series of disappearances in Jamaica, attack and seemingly kill Godzilla.

With Godzilla seemingly dead, the team journey to Jamaica to help the U.S. military investigate the ongoing disappearances in Jamaica. The team discover that a group of giant squids and a hideously mutated crustacean — Crustaceous Rex — is responsible and Godzilla (who has survived the attack) arrives to fight the beast off. Nick must now battle to help Major Hicks destroy C-Rex, and then convince him Godzilla is more useful alive than dead.

H.E.A.T. are called to help the Central America Republic of Costo Rojo deal with "El Gusano Gigante", a mutated worm that is devouring untold amounts of crops. The country's ruler, General Albondiga, uses an experimental bio-weapon against the worm and Godzilla, but the worm is only strengthened by the attack. Mendel must synthesise an antidote for the poisoned Godzilla, then find a way to defeat El Gusano without Albondiga interfering.