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.

A mysterious creature lands on Earth from the Moon. It soon starts to wreak havoc on shipping and seems to be affecting the water currents globally. The team and Godzilla must stop it before it causes worldwide devastation.