On their way to visit an oil rig, the team is captured by a mad scientist, who clones people and animals. He intends to clone the team and use them to steal the oil and make him a fortune.
The team stumbles upon a German U-boat from World War I, trapped in an iceberg. Godzilla frees the U-boat and the team is shocked when they discover the crew inside very much alive. The crew believes the war is still on. The team convince them otherwise just when a giant octopus attacks.
The team is stranded on an island inhabited by a creature named Axor. Captain Majors, Quinn and Brock become slaves and put to work. It's up to Pete, Godzooky and Godzilla to rescue them.
The team gets caught in a strange-looking hurricane. They end up in a city in the clouds. The inhabitants there want Godzilla and the evil power dragon to battle each other. Meanwhile the inhabitants plot to rule Earth.
A cyborg whale, which is a prototype sub used for scientific purposes, gets a malfunction while Pete and Brock are inside. It seems the cyborg whale is on a collision course with Hawaii.
The team investigates a new island formed in the Pacific Ocean. The team is trapped inside a volcano, inhabited by giant lizards that eat lava. Godzilla can't come to their rescue because is trapped as well.
A mysterious creature from the Moon lands on Earth and starts a chaos. The team and Godzilla have to stop it because it's affecting the water currents globally.
The team encounters a hostile tribe that worships giant gold statues. The statues come to life and while Godzilla battles with them, turns into a gold statue too.
The team traces a missile which destroys a new satellite which leads them to an island near Australia. It appears the island is under the control of a terrorist organization. They are captured by the terrorists, who take them for spies.
The team is sent to investigate an UFO sighting in the Arctic. Captain Majors and Quinn are imprisoned by an alien group of ice people and Brock, Godzilla and Godzooky are frozen. It is up to Pete alone to rescue them and save the world.