In trying to combat the villainous Mr. Cool (a Mr. Freeze incarnate), whose cold rays freeze everyone into solid ice, The Blue Falcon accidentally drops his Falcon commumicator from his Falconbelt in trying to save Dog Wonder. Using the Falcon communicator device, Cool tricks B.F. into believeing he is Focus One, telling him Dynomutt is being recalled to the factory for a reprogramming. Dog Wonder is then programmed by Cool into an evil D.W., who nearly succeeds in ending Blue Falcon's career...and his life!
Blue Falcon and Dog Wonder encounter The Worm, an evil genius abetted by escaped convicts Bugsy Busby and helicopter thief Roto Chopper, seeking revenge against Big City. Swooping down on Big City Tech (scene of a freak accident years back when The Night Crawler, then Professor Ronald Hickman, was transmogrified from an intelligent scientist into a worm), The Blue Falcon and Dynomutt discover and try to stop the villains' attempt to pilfer a multimillion dollar computer. Despite a string of Dyno DumDums, The Daring Duo lure The Creepy Crawler and his even creepier cronies into a bizarre underground pursuit (where else would worms go?) and trick them into burrowing into Big City Prison.
A visit to Ma and Pa Skillet in Okefenokee Swamp results in another adventure for Scooby and the gang. Cousins Scooby-Doo and Scooby-Dum greet each other for the first time since they were puppies. The Skillets own a showboat restaurant which specializes in Funky Fritters and Fenokee Fizz Soda and is being terrorized by The Gator Ghoul, an alligator-headed monster with glowing yellow eyes that has scared away customers and employees alike.
Dog Wonder and B.F., teamed with the Scooby-Doo crimestoppers, meet Lowbrow, a villain desiring to be king of crime employing the knowledge from the books of Big City University to further his dastardly schemes. This primitive thief unwittingly leads Blue Falcon, Dynomutt and Scooby Doo and company to his lair, where they discover his latest plan: robbery of Big City Mint!
A Mexican vacation becomes a search for missing Aztec treasure for Scooby-Doo and the gang. The town of Cinco, supposed site of a gala fiesta, is deserted, what with its residents terrorized by a stone monster and the ghost of The Aztec God Of Contezuma. Searching for an ancient pyramid nearby, the gang find clues that lead them to a mysterious river barge and a cave where the treasure is being smuggled away.