Godzilla is throwing infantile tantrums and H.E.A.T. are growing worried about their ability to control him. When Audrey lets this slip on live TV, despite being told in confidence by Nick, their relationship looks set to be torn apart. Meanwhile, when called in to investigate extensive deforestation in the Amazon Rainforest, they discover that a mutated termite colony is devouring the forest at an alarming rate. H.E.A.T. must find a way to destroy the voracious bugs before they devour the entire rainforest.

H.E.A.T. is charged by the Pentagon to investigate the growing population of spiders near an Army base in the Canary Islands. The team quickly discover that a massive mutated female black widow spider has been laying millions of eggs. They must find a way to destroy the infant spiders and help Godzilla take care of the mother.

When Godzilla is accused of attacking New York, the military call in H.E.A.T. to help contain him. But Phillipe Roache has returned from France... with orders to terminate Godzilla. However, H.E.A.T. discover the real culprit is a hideous mutation called the Chameleon, genetically engineered by Cameron Winter (who has escaped from jail) to frame Godzilla. Can they stop Winter and reveal the truth before it's too late?