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 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.
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.
The team traces a missile, which destroys a new weather satellite. That leads them to an island near Australia. It appears the island is under the control of a terrorist organization known as COBRA. The team is captured by the terrorists, who take them for spies.
When a UFO lands in the Arctic, the team is sent to investigate. They find an alien group of ice people that plan to destroy the Earth with an asteroid with the size of the moon. Captain Majors and Quinn are imprisoned and Brock, Godzilla and Godzooky are frozen. It's up to Pete to rescue them and save the world.