As tension threatens to break up the H.E.A.T. team for good, major problems arise: a Giant Bat is terrorizing the countryside of Nigeria, the U.S. military has dredged the Leviathan ship from the bottom of the Pacific, and worst of all, the aliens are back.

H.E.A.T. are dispatched to aid investigation into the disappearance of a search party looking for oil in Antarctica.

In Miami, Godzilla, H.E.A.T., and Major Hicks battle Skeetera, a mutated bloodsucking mosquito-like insect who adapts the powers of the creatures she feeds on. As they attempt to contain the creature they are interrupted by the mutation rights fringe group known as S.C.A.L.E. (Servants of Creatures Arriving Late to Earth).