During a nice relaxing day at the beach, the team is caught off-guard by a twister. They trace its origins to an experimental energy experiment at a local power plant, as well as discovering strange tracks near the plant. When the twister strikes again, H.E.A.T. discover that a giant mutant shrew has been bonded to the twister, creating a 'Shrewster', and now the race is on to defeat it before its ravenous metabolism drives it to eat all of New York.

On their way to an expo in an attempt to win a research patent, the team meets a lost young girl named Meg. She asks the team to rescue her two brothers Steven and Kevin, who went into a silver mine where a gang of miners disappeared without trace fifty years before. While Monique is left babysitting Meg (much to her displeasure), the rest of the team encounters the Silver Hydra: a monster capable of encasing anyone unfortunate to meet it in silver, and able to regenerate itself every time it is harmed. Now the race is on to defeat the Hydra before Kevin, Steven, Elsie and Godzilla end up as lifeless silver statues.

While tracking Godzilla to Fort Armstrong, New Mexico the team discover that a gigantic mutated scorpion, called Ts-eh-go by the locals, is on the rampage. But when they try to contain the monster, they come under fire from U.S. military under the command of Colonel William Tarrington, an old friend of Hicks, who is out to destroy both Ts-eh-go and Godzilla. When H.E.A.T discover Ts-eh-go was created by the army's 'First Wave' program, and that Tarrington is planning to use the creature's offspring - codenamed 'Second Wave' - as bioweapons, H.E.A.T and Hicks must convince Tarrington to stop when the scorpions get out of control.