Willie the Weasel has created a formula that turns him into Mr. Hyde. While 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 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. Fred and the others find a clue (which turns out to be Willie the Weasel's glove), and Blue Falcon deduces that Willie is Mr. Hyde. Blue Falcon and Dynomutt have Mr. Hyde proclaimed mayor and pretend to turn themselves in so Mr. Hyde will lead them to his secret lair and trick him into showing them the antidote to the Hyde formula. Willie the Weasel and his canine partner-in-crime "Snitch" manage to escape. Blue Falcon and Dynomutt head to the Mayor's Mansion to stop Hyde from retrieving his stolen loot. The Mystery Inc. gang set up one of their infamous "Scooby Traps" while Blue Falcon and Dynomutt confront Mr. Hyde and Snitch. Dynomutt captures Snitch while Blue Falcon and the Mystery Inc. crew capture Willie the Weasel/Mr. Hyde. 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. Blue Falcon and Dynomutt end up assisted by Mystery Inc. into stopping 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 Worm and his henchman Grub use a digging machine to spring Bugsy Busby and Roto Chopper from prison in a plot to steal a super-computer.

An ocean-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 Blue Falcon, Mayor Gaunt, and the Chief of Police.

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

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

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

Swamp Rat and his henchman Mudmouth plan to flood Big City by using stolen pumps to send half the water in Bogmyer Swamp into Big City to start a crime spree. 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 another 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 Blue Falcon and Dynomutt. Now Blue Falcon and Dynomutt must defeat Ironface and find out Ironface's true identity.

The Red Vulture steals 2 of the world's most powerful super-jet engines, with plans to use them for his nefarious Vulturejet and in turn dominate the airways.

Fishface, Gimmick, Lowbrow, Queen Hornet, Superthug, and Worm have escaped from Big City Prison and had formed the Injustice League of America. They plan to commit a major crime spree and dispose of Blue Falcon and Dynomutt.

An evil genius of the airways named 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.