Phillipe makes for the radio in Anna's jeep in an attempt to contact General Hicks. Nick pleads with him to wait. They argue. A shot suddenly rings out! The radio shatters. Phillipe and Nick turn to find Anna holding a gun on the pair! Anna reveals that she stumbled upon Godzilla over a year ago and has since dedicated herself to studying and protecting the creature with an almost militant determination. She remains hostile towards the pair, especially Nick. Nick tries to convince her that as a fellow scientist, he wants to help preserve the species not destroy it. He tells Anna he's come to prove that Godzilla and its brood are not responsible for the marauding attacks in the vicinity. But Anna refuses to believe him. She recognizes Nick as the person responsible for the first Godzilla's death. Nick has no choice but to come clean. He finally reveals the secret he’s kept from Phillipe, that he rescued a juvenile Godzilla in New York two years before and helped it escape – the same full grown Godzilla that is now running loose with a brood of its own. Phillipe is speechless. He can't believe that Nick would allow one of the creatures to survive, especially knowing how rapidly they multiply. Phillipe is determined to carry out his threat of alerting General Hicks. Nick suddenly ducks behind the wheel of Anna's jeep and roars away. Realizing he has to do something drastic in order to win Anna's trust and prove to Phillipe that Godzilla is essentially harmless, Nick swerves the vehicle and drives straight for the towering fifty story creature. Phillipe and Anna watch in horror as Nick drives right up to Godzilla. A ROAR from Godzilla shatters every window in the jeep. Nick hops out and stands before the giant behemoth. Godzilla raises a foot, ready flatten Nick like a pancake when it suddenly stops short. Something about this particular human is familiar. In a touching scene, Godzilla recognizes its 'mother' and nuzzles Nick affectionately, much to the utter astonishment of Phillipe and Anna. Nick turns yells to the pair- "You see? He’s really very gentle!" At that moment, Godzilla delivers a 'welcome home' ROAR that knocks Nick off his feet.

Sydney, Australia. Another giant egg larva is discovered on the outskirts of the city. General Hicks mobilizes his troops and heads Down Under. Another disturbing message arrives. There’s been no word from Phillipe or Nick for some time. They seem to have vanished without a trace.

In the Outback, Nick has a new problem: Godzilla follows him everywhere. And wherever Godzilla goes, its babies are sure to follow. This makes for some amusing situations, especially when Godzilla insists on sleeping beside Nick. Having won Anna’s trust, Nick invites her to study the 'Godzillas up close and personal. She shares some of her findings with Nick, including the fact that a full-grown Godzilla is capable of reproducing only once, and that the size of the brood is determined by carrying capacity of the land. Nick wrestles with his blossoming attraction for Anna. After all, technically he's a married man (Nick's attempts at contacting his new wife and explaining his whereabouts are continually met with her screaming at him and hanging up). During this period, Nick tries to convince Phillipe that Godzilla is a docile and non-aggressive creature that attacks only when its young are threatened. All three are amazed at the tenderness Godzilla shows its young, especially to the Runt. Nick and Anna are certain they're witnessing the birth of a new natural order, that Godzilla is the next step in an evolutionary process accelerated by the nuclear testing fallout. Phillipe is beginning to come around, to believe that perhaps there is a place in the world for Godzilla after all.

But when Godzilla suddenly steals away one night leaving its sleeping brood, Phillipe once again becomes suspicious. The three follow Godzilla in Anna's jeep some twenty miles to the deserted North Coast where they watch the giant creature disappear into the ocean. Nick is heartsick. Is it possible Godzilla has been making the various raids in order to feed its brood? Are the Godzillas being fed a steady diet of human captives? If so, then there would be no choice left but to destroy them. Suddenly, the ocean is lit up from beneath by bizarre flashes of lights (this is actually the first clue we have that Godzilla can breathe fire). Schools of tuna swarm to the surface. Godzilla explodes out of the water, forcing hundreds upon hundreds of the fish onto the beach. Nick, Anna, and Phillipe watch the amazing spectacle as Godzilla continues to herd schools of tuna onto the beach! As dawn approaches, another incredible sight greets them – Godzilla’s brood appears on the horizon! Descending on the beach, the hungry Godzillas begin gorging on the stranded fish! Nick now has the proof he's come after. Even Phillipe has to admit he was wrong, that Godzilla is not responsible for the other attacks. But if not Godzilla, then who? Or better yet, what? In order to answer than question, the trio decide to take a little trip.

Monster Island. Godzilla's birthplace. Following Godzilla's death, a clean sweep of the island produced no other biological anomalies. For two years the island has been off limits to visitors, its water heavily patrolled by U.N. warships. Approaching the island Nick, Anna, and Phillipe don wet suits and scuba gear in an effort to slip past the blockade. Swimming toward the island, the three are suddenly engulfed by a giant shadow and are stunned to witness a blue whale three times its normal size glide silently past.

On the island itself, more strange discoveries await – a plethora of new species, some mutated beyond recognition. Even so, there's nothing on the island that seems capable of kind of destruction being reported around the world. Suddenly, the skies above them darken. A strange buzzing sound fills the air. What seems to be an approaching dark cloud turns out to be a huge swarm of mutated winged insects equipped with vicious mandibles and deadly wasp like stingers. The Buick-sized insects appear to be carrying something wrapped in their six spiny legs. Nick, Anna, and Phillipe watch in horror as the insectoids land and release their human captives.

When one man tried to escape he is immediately set upon and stung to death! Meanwhile, wingless termite-like insects swarm out of an underground nest and herd the human captives underground. Nick, Phillipe, and Anna prepare to follow. Suddenly, HORRIBLE SCREAMS emanate from the entrance to the underground nest! One by one they die out until an eerie silence is all that remains. And just when things can't get any worse, the QUEEN BITCH emerges from the opening; a HUGE and ferocious-looking winged insectoid that the other insects flock around, tending to her every need. She is one nasty bug (and not above dining on her own kind) As Nick, Anna, and Philippe look on, the Queen takes flight and disappears out over the ocean, heading for God-knows-where. A horrible realization sinks in. People are being abducted from around the world and brought to Monster Island to be used as food by these horrible insectoids. Nick and Anna conclude that Godzilla and its brood are the natural predators of these bugs. But because of man's interference, the natural food chain on Monster Island has been disrupted. With no controls through natural predation, these insectoids will continue to multiply and spread, threatening the entire world. Somehow, Godzilla and its brood must be led back to Monster Island in order to bring the insectoids under control and reestablish order and harmony in the food chain.

Phillipe suddenly becomes extremely agitated, insisting they return to the Outback at once. Nick and Anna are perplexed by their friend’s strange behavior. Phillipe tells them that Godzilla and its brood are in grave danger. The truth finally comes out. Philippe has tipped off General Hicks and the Global Task Force as to Godzilla's whereabouts. Nick and Anna are stunned. Why would he do such a thing? Phillipe reveals he was frightened by the number of Godzillas they encountered. Ironically, he had nightmarish visions of Godzillas taking over the world which is what prompted his actions. Nick feels betrayed. He and Phillipe fight, before Anna breaks it up. She tells them to settle it later. Time may be running out for Godzilla, and the world.

But they're too late. Nick, Anna, and Philippe return to a scene of agonizing devastation. Godzillas lie dead everywhere. The countryside is rutted and pockmarked from explosions. The surprise attack by the Global Task Force has come from ground and air. General Hicks and his troops are advancing on Godzilla and one last juvenile (the Runt) when Nick, Anna, and Philippe arrive on the scene. Nick races past the troops and missile launchers out toward Godzilla and the Runt, causing Hicks to call a cease-fire. Nick looks around at the carnage, at the valiant fight Godzilla put up to save its babies. With tears in his eyes, Nick turns helplessly to Godzilla: "I’m sorry..." The look in Godzilla's eyes is one of heartbreak and betrayal. It ROARS in anguish before suddenly burrowing underground and escaping with the Runt. Nick stands alone a midst the devastation, feeling sick… Meanwhile, Phillipe is congratulated by General Hicks. But Phillipe tells the General they've made a terrible mistake. By killing the Godzillas, they may have just doomed the rest of the world. Before General Hicks can respond, he receives a message from Sydney: something bizarre is occurring to the giant egg larva.