The team makes a fascinating discovery: A German U-boat from World War I trapped in an iceberg. After Godzilla frees it, the team is shocked to see the crew of the U-boat still alive and they also believe the war is still going. They manage to convince them the war is over, but then a giant octopus attacks the U-boat, with Pete and Brock inside. Godzilla must stop the octopus before the sub is destroyed.

The team becomes stranded on an island inhabited by a creature named Axor. Axor enslaves Majors, Quinn, and Brock and puts them to work. Pete, Godzooky, and Godzilla must find a way to destroy Axor and save the island's inhabitants.

The team gets caught in a strange-looking hurricane and end up in a city in the clouds. The inhabitants explain they are there to escape an evil dragon in their old world. Unfortunately, the dragon follows them there. To make matters worse, after seeing Godzilla defeat the dragon, the inhabitants turn hostile and want Godzilla so they can have him destroy the dragon. The team must rescue Godzilla and keep him from falling into the wrong hands.