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.

After a lightning strike, a cyborg whale -- a prototype sub used for scientific purposes -- suffers a malfunction and steams out of control with Pete and Brock inside. Even worse, the whale is on a collision course with Honolulu, Hawaii. The others and Godzilla must rescue Pete and Brock and stop the whale before it destroys Honolulu.

After the Calico runs aground in a river, the team discovers a valley full of giant insects. Godzilla is initially paralyzed by aBlack Widow Spider bite and the entrance sealed by a landslide. The team must find a way to escape and also prevent the insects from escaping the valley.