On a lonely Alaskan island called Pitkin, strange tremors have local scientists concerned. When the tremors turn out to be caused by the awakening of a long-dormant volcano that erupts to coat the land with burning lava, the scientists' concern turns out to be very justified. Their only boat destroyed by the resultant tidal waves, the scientists only hope of survival is in calling for help.

Meanwhile, aboard the good ship Calico, little Pete is looking for his playmate, the obese flying Scooby-Doo lizard-mutant, Godzooky, who loves to play games. Soon after finding him, however, Pete and the rest of the crew discover there are more important things to worry about than the whereabouts of a big dumb flying reptile—a gigantic tidal wave is coming their way! With destruction imminent, Captain Carl Majors turns to the best help he can find—Godzilla, whom he has constantly on standby and can summon at the push of a button. Carl buzzes Godzilla, who immediately bursts out of the churning waters with a mighty roar and lifts the Calico above the water with mere moments to spare before the tsunami rushes by.

After thanking Godzilla, the members of the Calico receive the distress signal from Pitkin and rush to help, the ship speeding across the ocean on hydrofoils. Soon after they arrive, they convene with the scientists and decide the best course of action is to go into the active volcano via some lava tubes that they spotted during a flyover in a helicopter. They must find out what is causing the volcano to erupt and do something about it, or risk the eruptions spreading throughout all the volcanoes in the area. And somehow they missed the giant red pterodactyl that burst from the volcano and roared and flapped its wings while they were flying overhead.

As the scientists and Calico crew members enter the lava tubes, Godzooky soars after them, wanting to join in the fun. Pete, worried about the big lug, flies a helicopter after him—apparently he got his pilot's license at ten years old. Pete, Godzooky, and the rest of the gang have an adventure in the volcano—and discover the Firebird, the gargantuan red pterodactyl from before that, more than anything else, likes to flap its wings and roar a lot. The creature has a long neck, a big yellow beak and crest on its head, a sizable lower body, and a long serpentine tail. Thankfully, it's too dumb (or nice) to attack the humans, even when Godzooky flies right under its nose with Pete on his back. They all escape back outside and flee to the Calico—but the Firebird is close behind, bursting from the fire mountain and screaming loudly.

Captain Carl Majors panics, even though the Firebird has done nothing whatsoever to him or his family, and signals Godzilla, who is always up for a fight. The two monsters go at it, with the Firebird initiating attacks with his squiggly heat ray attack that appears to be about as dangerous to Godzilla as standing in front of a microwave is to us. Godzilla returns in kind, letting loose with his atomic eye lasers. The Firebird flies away from the blasts, but then circles around and carries the Big G through the air in its talons. Eventually the two monsters face off on land, posing and roaring until Godzilla falls off the cliff into the water and the fight is over.

The Firebird retreats, flying to the North Pole, but the Calico takes chase because they suspect that the Firebird is going up to that frozen tundra where hardly any life can exist to lay its eggs. The result of this single nesting would then be the subjection of the earth under millions of Firebirds.

Using a heat tracking device, the Calico tracks the Firebird to its snowy location and then summons Godzilla again. The two prehistoric saurians have another big throwdown that doesn't seem to be going anywhere until Godzooky enters the fray, getting blasted at by the Firebird's fire breath before getting knocked out cold against the ice by the reptile-bird's tail. Godzilla gets really miffed and drags the Firebird underwater, where he and the reawakened Godzooky manage to trap the bird with boulders in a cave. Everyone rejoices because they have saved the day again, until Godzooky tries to make a landing on the boat and nearly smashes into it. Thus the monstrous misfit is relegated to a little raft that is towed behind the Calico.