While on a romantic cruise to Alaska, Nick and Audrey's ship is attacked by a mutated turtle, but they are saved - not by Godzilla, but by Komodithrax, a mutated Komodo dragon. When Godzilla heads for Alaska to find Nick and H.E.A.T. follow, they make a shocking discovery: Godzilla and Komodithrax are in love, and Godzilla has become surrogate father to an egg laid by Komodithrax. But with the menacing turtle still nearby, and the U.S. military ordered to destroy all monsters in the area, can Nick and the team protect the two gargantuan reptilian lovers?

While fighting a giant mutant germ named Bacillus, Godzilla is infected by the bacteria and left fighting for his life. While Elsie, Randy and Mendel create an antibiotic to weaken the bacteria, Nick and Monique must enter Godzilla's body and destroy the infection at its source before Godzilla dies.

When Elsie's estranged parents come to New York for her spoiled sister's wedding, she is forced to attend as maid of honour instead of helping H.E.A.T capture a mutated manta ray. When the military's battle with the creature ends up interrupting the wedding, Elsie is determined not only to catch the creature, but to prove to her parents she is not the screw-up they think she is.