While Craven is laid up sick back at H.E.A.T. headquarters, Nick, Randy, Elsie and Monique assist Godzilla in a battle with a Mutant Jellyfish. The Heat-Seeker is engulfed by a mysterious storm which propels the team into a bleak, post-apocalyptic future where Godzilla is dead and the world is dominated by genetically engineered, 5-legged mutations known as Dragmas.

Shady promoter Maximillian Spiel entertains wealthy ticket holders with a series of “cage matches” between giant mutations like the Shrewster and the Giant Centipede. For his next bout, Spiel sets his sights on the “ultimate monster”… Godzilla.

In Miami, Godzilla, H.E.A.T., and Major Hicks battle Skeetera, a mutated bloodsucking mosquito-like insect who adapts the powers of the creatures she feeds on. As they attempt to contain the creature they are interrupted by the mutation rights fringe group known as S.C.A.L.E. (Servants of Creatures Arriving Late to Earth).

On the Arabian Peninsula, a team of archeologists led by Professor Abrim Kasam unearth an ancient statue of the flying lion Norzzug, the guardian of the ancient city of Amon-Ra. When restoration specialists spray the statue with an anti-oxidant solution, the iron-skinned creature suddenly comes to life.

A traveling carnival arrives at Madison Square Garden, and it's run by a crooked ringmaster known as Theodore P. Bunkum, who specializes in putting various captured mutations on display for public amusement. Bunkum places a hefty bounty on Godzilla, determined to add this most famous mutation to his carnival side show, and this incites H.E.A.T. to attend one of his shows, where they are quickly appalled by his treatment of the various mutations featured in it.

While on a romantic cruise in Alaska, Nick and Audrey’s ship is attacked by a Giant Turtle.

A new and deadly mutation, a plant-like creature known as Bacillus (who may have been inspired by Biollante), appears and begins wreaking havoc, prompting H.E.A.T. to call upon Godzilla. During the battle, Godzilla is seriously injured and rendered catatonic as the result of being injected with a highly dangerous form of mutated bacteria by Bacillus. In order to save their kaiju ally, Tatopoulos and Monique travel within Godzilla's body in order to carefully exterminate all of the mutant bacterium. Now fully healed, Godzilla attacks Bacillus anew, and eradicates the creature with his incendiary breath.

Elsie is suffering from a family problem of a personal nature, along the lines of sibling rivalry: her sister's wedding is soon to take place, and she is chagrined due to the disproportionate amount of attention and familial adoration that her sister has received in contrast to her. Further, she feels that her family has little respect for her choosen vocation, i.e., her activities with H.E.A.T. [that must be quite a hard family indeed to show a lack of appreciation for a daughter who has routinely risked life and limb for her planet by investigating and battling dangerous, life threatening giant monsters, and even helping to thwart an alien invasion! Her sister must truly be the world's most talented ass-kisser].

H.E.A.T. investigates a gigantic caterpillar-like mutation known as the Megapede, who is rampaging through the neighbor states of Illinois and Indiana. Godzilla is called upon to render assistance, but the Megapede sprays a form of poisonous foam, and also has poison producing spurs along its many legs, both of which serve to keep the Kaiju King at bay. The mega-insect finally climbs atop a building, forms a cocoon, and transforms into a huge winged insectoid creature with the habit of disrupting radar frequencies by rubbing its wings together, thus wreaking much havoc. H.E.A.T. concocts a poison neutralizing foam, which it spreads on the kaiju's wings, allowing Godzilla to attack and defeat the creature more easily.

H.E.A.T. investigates the legendary “Area 51” in Nevada and discovers its true secret is not alien landings, but giant mutated desert creatures created by decades of underground nuclear testing.

H.E.A.T. tackles a gigantic mutant shrew-like creature, which has somehow merged itself with an artificially generated, experimental tornado, enabling it to transform itself into a living vortex at will (Elsie wittily dubs the whirling beast 'The Shrewster'). In order to maintain its ultra-fast, whirlwind powers, the Shrewster is forced to rapidly consume three times its body weight per day, thus causing it to greedily devour every organic food source in its path, effectively making it an extremely dangerous menace. Because of its ability to transform itself into an organic tornado, Godzilla is unable to get at the beast, and Tatopoulos ends up trapped in the Shrewster's vortex. However, soon after becoming trapped, he activates a device that Craven crafted, which was designed to dissipate the vortex's cyclonic forces, and this succeeds.

While conducting another creature investigation in the valley of Blind Rock, Wyoming, H.E.A.T. meets up with a girl whose brother went missing after he entered an abandoned mine in the area where the sightings took place. Upon entering the mine themselves, the group discovers one of the strangest mutations they have yet encountered, a huge two-headed kaiju known as the Silver Hydra, on account of the fact that it has the ability to spurt a silvery fluid that hardens once it surrounds a living being, thus transforming them into the equivalent of a silver statue, a fate that obviously befell the girl's brother.

While tracking Godzilla to Fort Armstrong, New Mexico the team discover a gigantic mutated scorpion, called Ts-eh-GO by the locals, is on the rampage.

Another new and dangerous mutant species appears on the scene, this time in the form of gigantic hummingbirds that attack planes flying over San Francisco. Worst of all, this mutant avian species is able to render themselves invisible via the hummingbird trait of flapping their wings faster than any other bird species in the world. As a result of their ability to cloak themselves so as to be invisible to the unaided eye, Godzilla is unable to see the creatures in order to attack them.

During its latest creature investigations, H.E.A.T. splits up into two teams, one of which investigates a group of mutant parasitic organisms in Florida, whereas the second group handles a case of a giant, mutated, and rapidly growing multi-tentacled fungi-like creature in Michigan.

As a result of an oil platform in the Gulf of Mexico exploding, a mutant seemingly composed of living fire emerges. As this creature goes on a rampage in the area looking for more combustible substances upon which to feed, H.E.A.T and Godzilla intervene. However, the creature grows larger and more powerful as a result of absorbing and feeding off of Godzilla's powerful incendiary breath.