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.

H.E.A.T. travels to Central America to investigate their latest creature sighting and they encounter a dangerous, subterranean monster that resembles something of an enormous hybrid of an earthworm and a slug.

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.

A new form of microorganism is created, designed via genetic engineering to consume oil spills and other manmade pollutants in New York City but it mutates and becomes an enormous, ever-growing mass of protoplasm that devours everything in its path.

A colony of huge mutant rats appear on the scene, wreaking havoc on the sprawling metropolis at night. Soon, the problem is escalated as Godzilla appears and begins to attack the rats in defense of his territory, thus causing more destruction to the city.

A powerful gigantic monster possessing the ability to discharge crackling bolts of destructive electrical energy suddenly appears in the middle of New York City and begins wreaking havoc, only to mysteriously disappear in the midst of an attack.

Nick and H.E.A.T. go deep beneath the sea in order to investigate the mysterious disappearance of noted scientist Dr. Alexander Preloran and his own research team, and there H.E.A.T. discovers a hidden spacecraft belonging to a race of advanced, hostile non-humanoid aliens that hope to conquer the Earth with the help of a pet giant monster.

H.E.A.T. journeys to an island in the course of one of their creature investigations, and there encounter not only mutated carnivorous plants, which attack large animals, including human beings, but also discover that the island is ruled by a swarm of gigantic bees, all under the direction of an ultra-huge queen. Godzilla himself engages the queen, as H.E.A.T engineers the destruction of the island to protect the outside world from the menace of the giant bees, and both Godzilla and H.E.A.T. escape from the island just in the nick of time.

Mexico is under siege from a mutated beast that resembles a gigantic winged lizard, which is named Quetzalcoatl after the mythological Aztec deity whom it also resembles [by coincidence, of course]. H.E.A.T. investigates, and discovers that the flying beast is guarding a nest whose eggs are soon about to hatch, thus creating the threat of numerous such creatures terrorizing the planet.

H.E.A.T. journeys to Loch Ness in Scotland, in order to search for (what else?) Nessie, the famed Loch Ness Monster herself. This is because the famed Loch Ness Monster has eschewed her usual shy mein in order to inexplicably attack a Scottish scientific institute.

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?

During the search for the Bat, H.E.A.T. discovers that many of the previous mutations which they and Godzilla battled are still alive, and have now re-appeared as a result of the aliens taking control over each of the creatures as part of their plan to conquer the planet. The aliens soon have all of the mutations under their control, including Godzilla, and they use the kaiju, backed up by several marauding alien ships, to beat humanity into submission by attacking the major cities of the world.

Tatopoulos finds a way to free the H.E.A.T. team from the telepathic control of the aliens via disrupting the tachyon emissions which the octopoid extraterrestrials use to control minds [actually, tachyons are hypothetical sub-atomic particles, mentioned frequently in sci-fi shows such as the various Star Trek series, which have the unique property of traveling backwards in time, and thus have nothing to do with psychic phenomena, but instead tend to be present in time travel phenomena and chronal anomalies of various sorts; it would have been more realistic to have the aliens utilize technology that generated psions, another very hypothetical particle, which is said to carry psychic energy, and is believed by some parapsychologists to be responsible for various psychic phenomena such as telekinesis, precognition, telepathy, etc., and thus could indeed affect organic brains in such a manner as to control them].

Yet another scientific research team disappears, this time in the South Pole [geez, these research teams are a royal pain in the posterior, but what would sci-fi and horror series and films ever do without them!], and yet again, H.E.A.T. travels there to investigate, suspecting a creature problem again [just think of all the work that H.E.A.T. would miss if not for vanishing research teams!].

Tatopoulos discovers that Godzilla is undergoing unusual changes, growing physically smaller, and also acting nastier and less subject to his control. Upon further investigation, he discovers that the source may be related to reports of giant mutant termites in the Amazon Rain Forest. Upon traveling there, Randy concocts a device that emanates audio signals of a specific frequency, which creates mass confusion among the termite colony. As a result of this, Godzilla returns to normal.

On yet another investigation to the Caribbean [the fringe benefits of working for that team are excellent!], H.E.A.T. discovers a nest of huge, mutant spiders, which are controlled by a single spider that is much larger than the rest [this is unusual, since spiders are independent organisms and do not live in hives or colonies as various insects, such as bees and ants do, and are thus not ruled by a ""queen,"" which is a fact that was also ignored by the spider-paranoia flick Arachnophobia]. As Godzilla battles the huge ""master"" spider (possibly inspired by Spiega), danger strikes when Craven utilizes a new (and ludicrous) device designed to enable him to ""communicate"" with Godzilla, which actually has the dangerous (and embarrassing) result of causing Godzilla to retreat, thus leaving the island and the H.E.A.T. team once again at the mercy of the spider infestation.

When it appears that Godzilla has gone savage, and is now attacking New York City in the same manner as his predecessor did (in the Centropolis film Godzilla), Major Hicks is once again called upon to destroy the Kaiju King.

A strange object descends from outer space, and merges with a child's remote control truck. The object turns out to be a being that can somehow assimilate technological machinery within itself, thereby taking on the attributes of said technology. Hence, the entity becomes progressively larger and more powerful, thus being labeled the Juggernaut [not to be confused with Cain Marko!].

Monique learns from Major Hicks that a bizarre new life form was created via genetic engineering, and was now left abandoned in an old laboratory in Brazil. She convinces her allies in H.E.A.T. to go and investigate, and they soon discover that the creature is actually a DNA absorbing beast known as the Mimic, which can, as its name suggests, take on the exact physical and behavioral attributes of any living creature that it comes in contact with. The Mimic thus imitates the appearance of all of the H.E.A.T. members in turn, and paranoia reigns as everyone in the group must continuously be wary of each other as they search for a means of destroying the creature, since nobody may be who they appear to be. Finally, the Mimic imitates the size, appearance, and power of Godzilla [so much for the law of conservation of mass!], and the two Big G's battle it out, fighting each other to a standstill in the process.