Nick is worried that one of Godzilla's egg might have survived the events of the 1998 Godzilla movie. When Godzilla's offspring hatches indeed from a single surviving egg, Nick and his science team known as "H.E.A.T." must stop it.
It turns out that Godzilla's offspring, also named Godzilla, thinks Nick is its parent, since he was there when it hatched. Nick and his team use this to get Godzilla to help them fight a new giant mutant threat - angry deep-sea squids.
Costo Rojo, a fictional country in Central America, is plagued by a giant mutated worm, El Gusano Gigante. H.E.A.T. and Godzilla help, but the countries strongman, General Albondiga, attacks it with bio-weapons and makes things worse.
H.E.A.T. must resolve the mystery behind the strangest mutant they've ever seen - the so-called Crackler that uses electricity in its attacks. Is it a product of a freak mutation, science or just one man's dream?
A seemingly dormant giant alien spacecraft that's been at the bottom of the Pacific Ocean for 65 million years is discovered and dubbed Leviathan. H.E.A.T. is sent to find the scientist who went missing while exploring it.
A mutant creature that resembles Quetzalcoatl, a Mesoamerican deity that looks like a feathered serpent, is attacking villages in Mexico. Elsie, a member of H.E.A.T., has personal interest in this case.