From their secret base on Isle Del Diablo, the aliens assemble their forces. H.E.A.T. desperately fights to resist, but are easily defeated. Once captured and brought to the aliens, they are told that the monster army — including a brainwashed Godzilla — will be used to attack major cities across the world in preparation for a full-scale invasion of Earth. At its head marches the aliens' ultimate weapon: Cyber-Godzilla.

As the aliens and their monster allies attack Earth, H.E.A.T. escapes captivity. They battle to defeat the alien onslaught and free the monsters from their control to help humanity fight back and save the planet from conquest.

A trip to Japan to investigate a number of mysterious disappearances leads to a battle of wills between H.E.A.T. and the Japanese military, who perceive Godzilla to be a threat. However, the real threat is revealed to be anophidiaphobic's nightmare: the mutant King Cobra has escaped from Monster Island. Things lead to a climactic showdown in Tokyo between him and Godzilla.