Just when the first Godzilla is destroyed, another one is born. Imprinting on Dr. Nick Tatopoulos, the infant eludes the military then follows Nick to his waterfront headquarters.

In the wake of Godzilla’s apparent death, Nick convinces H.E.A.T. to stay together to study other mutations around the world. The team travels to Jamaica to investigate attacks on boats and swimmers from what appears to be a giant squid.

Nick is contacted by Cameron Winter, an old college buddy, with an offer of hiring H.E.A.T. Allegedly towards this end, Winter entices Randy to plant an experimental computer-operated device upon Godzilla that, unknown to Randy and the rest of H.E.A.T., is actually for the purpose of controlling Godzilla.

The aliens finally launch an assault on earth, using a powerful device to render all of earth's monsters under thier control, even the original Godzilla returns from the grave, now a partial cyborg, can the present day Godzilla bring himself to attack his ""Mother"", or will he turn against the team?