After Godzilla battles robotic insects, the team encounter their creator: Cameron Winter, a powerful technology mogul, and an old rival of Nick's from college. He wants H.E.A.T. to work with him, but Nick refuses, suspecting his old enemy has ulterior motives. But can he find out what they are before Winter's schemes have fatal consequences for Godzilla?

In response to a sanitation workers' strike, a colony of petroleum-eating microbes, controlled by nanotechnology, are released to try to curb New York's garbage problem. Unfortunately, the microbes quickly grow out of control and now the team and Godzilla must find a way to stop the colony before it devours Manhattan.

The team not only have to contend with a plague of mutated giant rats roaming the sewers of New York, but a trio of redneck hunters seeking to make Godzilla the ultimate hunting trophy.