H.E.A.T. heads for Scotland after Dr. Hugh Trevor (voiced by Roddy McDowall) of the Pisces Marine Research Institute claims his facility was attacked by theLoch Ness Monster. Once Nick is convinced of Nessie's existence, he discovers that the facility is hiding a terrible secret: Trevor has captured Nessie's baby and plans to sell it on the black market. Now the team must convince Godzilla to work with Nessie if they are to save her young and ensure her safety in Loch Ness.

As tension threatens to break the H.E.A.T. team up for good, major problems arise: a giant bat is terrorizing the countryside of Nigeria, the U.S. military have dredged the Leviathan ship from the bottom of the Pacific, and worst of all, the aliens are back, with an army of monsters under their control and plans to conquer the Earth.

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.