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.
