At some nameless scientific facility, the resident scientists are collecting solar energy and opening a new dam. A meteorite falls nearby and leaves a huge crater. The crater is not radioactive, but the brainy humans find massive tracks leading from the crater to a nearby pair of trees. The scientists are tired from a long day of thinking, though, and decide to go to sleep. But after they leave, one of the trees begins to glow and beep—and then it turns into a centipede monster with a pokey tail!

The Calico, meanwhile, is going down a river known as the Big Silty. The crewmembers hear a big splash, and it is revealed that Godzooky is diving for fish, but all he gets is a bunch of seaweed and garbage. They are on a trip to Sundance Mesa, and they soon come to the Sundance Mesa dam.

It's at that time that they spot the giant centipede from space. The multi-footed monstrosity walks across the dam, breaking up the concrete, then cuts through the roof of a nearby building. Captain Carl Majors solves his problems the way he always does—he calls Godzilla. The energy beast, not knowing about the coming danger, begins soaking up the energy from the dam, which makes it grow. At that moment Godzilla bursts from the water and roars and thrashes his arms a lot.

The two monsters roar at each other. They both lunge, and the centipede wraps around Godzilla, who pushes him off like an unwanted piece of clothing. The energized insectoid then runs away on his many little legs. Godzilla flames at the sensational centipede, and the energy beast fashions a ball of energy with his claws and throws it, missing Godzilla but blowing up the mountain behind him. Godzilla walks toward the monolithic arthropod, but busts a chunk out of the dam he is traipsing across, giving the energy beast the chance to chuck another energy ball, which hurts Godzilla badly and makes him look really tired and drunk, leading to the heroic irradiated dinosaur's retreat.

It's up to Godzooky to snap Godzilla out of shellshocked stupor with an obnoxious roar. Godzooky's blaring honks work like a charm, and Godzilla, back in action, uses his laser eyes to fix the dam, making it just like new. But our monster Godzilla is still feeling a bit queasy and sinks into the water.

Our human heroes talk with the lazy scientists and learn about the meteorite. The scientists show off their sonar energy collector and how it is like a big overgrown mirror. Godzooky takes advantage of the opportunity and makes scary faces in the reflection.

Somebody notices that one of the trees that used to be growing near the laboratory is missing. The scientists are called back to the facility and discover that Godzilla (covered with crackling energy, much like the centipede had pulsing across his exoskeleton before) is attacking the power station! Our heroes need to think of a way to get Godzilla away and save Mason City. They fly in a helicopter and yell at the errant lizard using a bullhorn, but Godzilla won't listen and swipes at the chopper with his claws, forcing them to make an unplanned landing.

Our valiant heroes decide the best plan then is to take the energy away from Godzilla and thus remove the reason for his assault, and the scientists divert all electricity away from the power station. Godzilla roars a lot and smashes some stuff and walks off. The scientists and our heroes decide they must stop Godzilla and the energy beast from destroying any more power buildings—and it is then that someone mentions that there is a nuclear power plant nearby! Godzooky and Pete are sent back to the mesa—naturally, the two rascals don't obey for a moment and decide to help in the never-ending creature conflict instead.

Godzilla, meanwhile, starts smashing cars and throwing them around, marching to attack the power plant. Pete tells Godzooky to roar and bring Godzilla back to his senses, like he did before. But when Godzooky bleats his plaintive cry, instead of curing the ballistic nuclear-hungry lizard, he calls the real Godzilla from the sea! Real-deal Godzilla hurries over and gives the fake Godzilla a hug. They struggle mightily, and the authentic Godzilla blasts his deceptive twin with fire breath. Fake Godzilla shoots real Godzilla with those energy beam eyes, and then zaps the nuclear reactor. Godzooky flies up to look at the two Godzillas, completely confused as to which is the real one— until the fake one bashes Godzooky, and the true heroic lizard saves his hinder. Unfortunately the real Godzilla hasn't gotten any smarter, and his next attempted attack on fakey G ends with the heroic radioactive dinosaur buried in rock. False Godzilla retreats back to the dam.

Fake Godzilla finds the giant mirror near the dam and gets mad, seeing himself and thinking he sees the real deal. He blasts the mirror with his fire breath and then takes a flying leap right through it. The authentic Godzilla catches dumb-fake Godzilla by surprise and grabs him from behind. As Godzilla holds the deceptive dinosaur, the fake G turns back into a centipede and loses size apparently from lack of energy. The somewhat more bug-sized centipede dashes away into the meteorite crater and down a sizable crack in the ground. Godzilla, yet unsatisfied with his victory, rips open the crack and uncovers the centipede and a flying saucer! The centipede crawls into the shiny UFO and then Godzilla takes it in his hands like an intergalactic frisbee and throws it into outer space! "What an arm!" says Brock.

With the danger at an end, Brock jovially inquires if Godzooky is still looking for fish. But no, not anymore! Now he's after innertubes. Godzooky has made a raft of inner tubes and starts riding them, towed behind the ship!