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.

When a strange electrical creature known as the Crackler attacks seemingly random locations in Manhattan, the team investigate. But the Crackler isn't behaving like the mutations H.E.A.T. have fought before, and what is its connection to mild-mannered insomniac Sidney Walker?