A colony of huge mutant rats appear on the scene, wreaking havoc on the sprawling metropolis at night. Soon, the problem is escalated as Godzilla appears and begins to attack the rats in defense of his territory, thus causing more destruction to the city.

During the search for the Bat, H.E.A.T. discovers that many of the previous mutations which they and Godzilla battled are still alive, and have now re-appeared as a result of the aliens taking control over each of the creatures as part of their plan to conquer the planet. The aliens soon have all of the mutations under their control, including Godzilla, and they use the kaiju, backed up by several marauding alien ships, to beat humanity into submission by attacking the major cities of the world.