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.

The team are called to San Francisco, where a group of giant mutated hummingbirds are attacking aircraft. The creatures move too fast for the naked eye to see them, making them impossible for Godzilla to fight. Now Mendel must rig up a special set of goggles that will allow Godzilla to see the birds, giving him a chance to fight back.