The Cyborg Whale was built by a government party to farm and harvest plankton. Brock and Pete are aboard it to do a test drive. When the Cyborg Whale is struck by lightning during a thunderstorm, the Whale's computers are damaged and it heads to Honolulu, Hawaii. Godzilla is called, but he can't use his powers against the Cyborg Whale so he doesn't hurt Brock and Pete, who are trapped inside.
Brock and Pete manage to open the Whale's porthole and are safely transported away by Godzooky. Now, Godzilla bends the Cyborg Whale's rudder, forcing it to swim in circles until it runs out of fuel. The Cyborg Whale is then taken away for repairs.