Willie the Weasel has created a formula that turns him into Mr. Hyde. While the Blue Falcon and Dynomutt are on the trail of the mysterious Mr. Hyde, they encounter the Mystery, Inc. gang and Scooby-Doo (who are unaware that Mr. Hyde is a supervillain and not one of their typical "spooks"). In The New Scooby-Doo Movies-fashion, they team up with the Blue Falcon and Dynomutt (who happens to be Scooby's hero) to stop Mr. Hyde, who has threatened to turn the population of the entire city into "Mr. Hydes" unless he is proclaimed mayor. Note: This episode is a crossover between Dynomutt, Dog Wonder and Scooby-Doo.

A caveman-like criminal named Lowbrow wants to become the King of Crime and steals some books that will help him in his quest. The Blue Falcon and Dynomutt end up assisted by Mystery, Inc. to stop Lowbrow. Note: This episode is another crossover between Dynomutt, Dog Wonder and Scooby-Doo.

The Gimmick is a criminal mastermind who uses his prowess of gadgets to create havoc in the city and dares the police to stop him from stealing a train car with a prince inside. Note: Mumbly makes a cameo at the end of the episode.

A talking worm called the Worm and his henchman Grub use a digging machine called the Wormborer to spring Bugsy Busby and Roto Chopper from prison in a plot to steal a super-computer.

A fish-themed villain named Fishface plans to steal Big City's oil and hold it for ransom.

Manyfaces uses his talent for disguises to trick Dynomutt into arresting the Blue Falcon, Mayor Gaunt, and the Chief of Police.

Superthug and his henchman Zorkon have created a super-dynamic steel skeleton and plan to use it to steal Big City's steel supply to mass-produce an army of steel skeletons.

The Blue Falcon loses his Falcon Communicator while he and Dynomutt are fighting Mr. Cool. Mr. Cool then makes the Blue Falcon think that he is F.O.C.U.S. One claiming that Dynomutt needs to be recalled to where he was made. With Dynomutt reprogrammed and now under his control, Mr. Cool has Dynomutt dispose of the Blue Falcon while he initiates a plot to freeze Big City.

The Blue Falcon and Dynomutt attempt to get evidence that will put the Queen Hornet in prison.

The Swamp Rat and his henchman Mudmouth plan to flood Big City by using stolen pumps to send half the water in Bogmeyer Swamp into Big City to start a crime spree. The Blue Falcon and Dynomutt, team-up once again with Scooby-Doo and Mystery, Inc. to stop the villains before Big City becomes Bog City. Note: This episode is the third crossover between Dynomutt, Dog Wonder and Scooby-Doo.

A hack movie director named Eric von Flick plans to make a movie called The Total Destruction of Big City starring his robotic creation, Tin Kong.

A mysterious criminal named Ironface seeks revenge on Big City by capturing the District Attorney, the Warden of Rockatraz, Detective Malloy, Mayor Gaunt, Judge Grater, Chief of Police Grisby, and the Chief Prosecutor, as well as the Blue Falcon and Dynomutt who it blames for its incarceration. When the Blue Falcon and Dynomutt get captured, they work to free themselves and the other captives. Then they defeat Ironface and its minions as the Blue Falcon unmasks Ironface to be Serpent Lady.

The Red Vulture steals two of the world's most powerful super-jet engines, with plans to use them for his Vulturejet and, in turn, dominate the airways.

Fishface, Gimmick, Lowbrow, Queen Hornet, Superthug, and Worm have escaped from Big City Prison and formed the Injustice League of America. They plan to commit a major crime spree and dispose of the Blue Falcon and Dynomutt. Note: the titular villain group has no connection to the DC Comics villain group of the same name.

An evil genius of the airways named the Blimp is stealing Big City's supply of helium.

The Prophet sets up his own disasters, which he can predict for Mayor Gaunt and charge him $500,000 for every prediction he wants to know.