Willie the Weasel creates a formula that makes him into a Mr. Hyde. He uses this to rob a jewelry store and then when he's outside, he uses the antidote to revert back to normal. Blue Falcon and Dynomutt receive the news about this new threat and they take off in the Falcon Car. Blue Falcon deduces that Mr. Hyde will strike at the Crown Jewels exhibit and he is correct, however, Mr. Hyde uses his formula on the guards at the museum and makes them Hydes. Then he tells them to steal the jewels for themselves and he leaves. Blue Falcon and Dynomutt arrive and capture the Hydes and then Dynomutt malfunctions and falls for a trap set by Scooby and the gang. Blue Falcon and the gang discuss what has happened and he welcomes their help on the case.
They all go to the mayor's office and discuss their next step. Fred, Daphne , and Velma go to the museum to look for clues while Blue Falcon, Dynomutt, Shaggy, and Scooby go to Professor Orville's lab to see if he can come up with an antidote for the Hyde formula. Unknown to them, Mr. Hyde is outside and hears everything and when they get to the lab, Mr. Hyde changes Professor Orville into a Hyde. Blue Falcon corners the real Mr. Hyde but another one of Dynomutt's malfunctions allows him to get away.
They return to city hall and Fred gives Blue Falcon a rubber glove they found at the museum. Dynomutt processes the glove and they discover that Willie the Weasel is Mr. Hyde. It seems that Mr. Hyde wants the job as mayor of the city. The mayor refuses his demand and Mr. Hyde starts changing citizens into Hydes. Blue Falcon suggests that they give in to his demand but he has a plan.
Mr. Hyde takes over as mayor and then sprays Blue Falcon and Dynomutt with his Hyde formula and changes them into Hydes. They then go to his apratment where Blue Falcon-Hyde asks him how he will go to other cities without being recognized and Hyde shows them his antidote. This is what Blue Falcon was waiting for and shows his real face. The Hyde formula never got to him or Dynomutt because they were wearing masks at the time he sprayed them. Willie springs a trap and thinks that they won't get out, but Dynomutt breaks them out.
They then get with Scooby and the gang and they make a plan. Blue Falcon and Dynomutt enter the house where Hyde is and get the antidote and Dynomutt catches Hyde's dog, Snitch and Hyde races off in the mayor's car. Blue Falcon then uses his device along with Dynomutt to capture Hyde.
Everyone is returned to normal and they all meet back at the mayor's office. Shaggy says that he forgot something, but can't remember what it was. Then Dynomutt malfunctions and falls into another trap set by Scooby and the gang and Shaggy remembers that they forgot to take down the trap.