After solving another mystery involving the Manic Minotaur of Mainsley Manor, Scooby and Shaggy take the rest of the gang [and Doc and her toys] to a comic book convention called the Mega Mondo Pop! Comic ConApalooza (featuring people dressing up as many Hanna-Barbera characters), held in San De Pedro, California, to enter a costume contest as their favourite comic book superheroes, Blue Falcon and Dynomutt, Dog Wonder. Fred is eager to see the new and darker Blue Falcon film, produced by Jennifer Severin, starring Brad Adams as the new Blue Falcon (which Shaggy and Scooby find revolting). Daphne tags along to complete her collection of toys called Littlest Fuzzies. Velma, although showing no interest in comic books, comes along to investigate a recent report about a monster-man lurking in the convention center. However, Shaggy and Scooby ignore this, believing that Velma is only mentioning this to ruin their weekend. At the convention center, they meet Hank Prince, the owner of a comic book store Shaggy visits regularly, and his nephew, Austin. They also find the actor of the original Blue Falcon show, Owen Garrison. They eagerly approach Garrison to get his autograph, but instead they listen to their favorite celebrity ranting about how the studio is planning to remove all the original Blue Falcon shows for the upcoming new Blue Falcon movie and are spooked off when Garrison swears revenge for being left out of Hollywood.
Later on, the gang goes to see the trailer of the upcoming Blue Falcon movie. During the screening of the trailer, the monster-man from the report, which Shaggy and Scooby immediately identify as Mr. Hyde, the villain from the original Blue Falcon television show. Mr. Hyde appears and unleashes a swarm of bats which terrorize the public, and vandalizes some of the convention booths including the new Blue Falcon booth [though Stuffy describes the incident as the coolest 3D ever]. During the chaos, Fred and Daphne manage to save some people from being crushed by a falling movie screen. After the entire public is evacuated from the building, the gang informs the head of security James Becker who they are and offer to help investigate the situation. At first, Becker declines the offer and orders the convention to be shut down, but changes his mind when the Mayor of San De Pedro named Ron Starlin orders Becker to keep the convention open because of the amount of money the convention raises.
The gang starts searching for clues by attending a party held by Severin. There, they see Garrison being taken away by security for trying to enter the party without an invitation causing the gang (except for Scooby and Shaggy, and Doc) to suspect that Garrison might be the villain; Doc slightly disagreeing with Fred, Daphne and Velma. While asking around for information, Mr. Hyde reappears and trashes the party with his pet the Hideous Hyde Hound. Also, Stuffy is very quick to guess Owen Garrison's condition for the Big Book of Boo Boos; I-want-my-revenge-itis.
The next day, the gang returns to the convention to wait for another Mr. Hyde attack. Fred first tries to find Garrison to question him, which in turn angers Shaggy and Scooby, who state that Garrison can’t be Mr. Hyde. The gang also meets Jack Rabble, a former contestant of a robot fighting show called Combat Bots who now makes a living signing autographs, selling robots, and sharing a booth with Garrison. In an attempt to prove their hero’s innocence, Shaggy and Scooby buy a spybot from Rabble and uses it to investigate the other suspects. They first show the others a recording of Severin boasting on how the Mr. Hyde incident has been increasing publicity for the Blue Falcon movie. The second footage has Adams talking about how he dislikes his role as the new Blue Falcon and hopes that Mr. Hyde will draw the public’s attention away from him giving him a chance to quit. They even have footage of Hank making a mysterious phone call in another language and found out from Austin that Hank has been sneaking off numerous times. Their investigation impresses, but also surprises the others, but mostly Doc. After showing their clues, Velma secretly gets rid of Shaggy and Scooby by giving them free passes to the VIP lounge so that they can question Garrison without them knowing. They also found out from Austin that the Mr. Hyde attacks are based on the original Blue Falcon animated episodes and that Mr. Hyde uses green ooze that turns people into monsters in his next appearance. Chilly and Stuffy tag along as well.
Meanwhile, Stuffy, Chilly, Scooby and Shaggy are scared out of the VIP lounge by the cook for eating all the food. They flee into the storage rooms where they find Mr. Hyde’s secret lair. Mr. Hyde attacks them with green ooze and chases them onto a big Frankenstein Jr. Balloon, which he uses to fly across San De Pedro. Mr. Hyde unleashes his green ooze on the entire town and at city hall, oozing them, and even the mayor. At first, Scooby and Shaggy panic, believing that they are going to become monsters but then realize that the ooze is just a harmless pistachio flavored foam. Angered and humiliated by this assault, the mayor fires the gang.
Later on, the gang watch a new report about the incident and learn that the premiere of the new Blue Falcon movie will now be held at the baseball stadium due to the increased danger levels. They also see security footage of Scooby and Shaggy cowering over the ooze, which they believed was turning them into monsters, and the footage has now become a viral video on the Internet. Ashamed by this, Scooby throws away his Dynomutt costume. Daphne then receives a phone call from Rabble, telling her that Garrison is missing. The gang head back to the convention centre, except for Scooby and Shaggy, who are too embarrassed to show their faces in public. However when they get there, they are denied access from Becker, by order of the mayor. With Doc's help, Austin manages to get them all in and then heads off to sneak into the baseball stadium and get a first glimpse of the movie, with Doc and the toys going with him. With Rabble’s help, Fred, Velma and Daphne find Mr. Hyde’s hideout and discover that Mr. Hyde has surveillance cameras of the whole convention centre as well as the baseball stadium. From there, they see a giant Mr. Hyde (another follow up to the original Blue Falcon animated series) rampaging in the stadium whilst stating repeatedly that no one will see this film.
Meanwhile, while getting something to eat, Scooby and Shaggy notice that people are fleeing away from the stadium, causing them to believe that they have a chance to enter into the stadium to find food without anyone seeing them. They run into the stadium only to find the giant Mr. Hyde chasing Austin and Doc. When Shaggy asks, "Where’s a hero when you need him?" Scooby regains his superhero instinct and rushes to confront the giant Mr. Hyde. Scooby and Shaggy manage to rescue Austin and Doc, but are booted into the air by the giant Mr. Hyde, and they land into a dump truck. Their slapstick performance ends up being recorded by a boy walking by, who intends to upload the footage on the internet, making them embarrassed once again. Fred, Velma and Daphne arrive and manage to bring down the giant Mr. Hyde. They find Garrison in the giant robot, suggesting that he was Mr. Hyde all along, however Garrison claims that someone knocked him out and placed him inside the robot in order to frame him.
It turns out that Garrison was telling the truth, when Doc, Scooby and Shaggy witness the real Mr. Hyde stealing an armoured vehicle. Scooby pursues Mr. Hyde and causes the armoured vehicle to crash into the giant Mr. Hyde robot. Mr. Hyde uses knockout gas on the security guards, the police and Fred, Velma and Daphne and then unleashes his Hideous Hyde Hound on Scooby. Garrison, while wearing the original Blue Falcon uniform, saves Scooby, destroys the Hideous Hyde Hound using the Falconcar, and stops Mr. Hyde from escaping just as Mayor Ron Starlin arrives. Garrison thanks Scooby for his assistance and Austin finds out that his uncle has been secretly going on a date with Nora Bingleton (a comic book fanatic who dresses up as Princess Garogflotach).
The gang unmasks the real Mr. Hyde, who turns out to be Rabble. Rabble explains that many years ago, he was banned from Combat Bots when one of his robots malfunctions and destroys the studio, forcing him to make his living by signing autographs at the comic convention. When Rabble found it difficult to rent a booth, he started sharing with Garrison to save money. Rabble was irritated with Garrison’s constant complaints about being unable to revive Blue Falcon and after hearing about the release of the new Blue Falcon movie, Rabble devised a plan to rob the entire convention. Using his knowledge on robots, Rabble designed the Mr. Hyde costumes, the bats and the Hideous Hyde Hound. He confirmed that he used the knockout gas on Garrison and then placed him in the robot, which was remote controlled. Rabble explains that the rampage at the stadium was done to diverge the traffic and force the armored vehicle onto an empty emergency route, where he could attack it. The armored vehicle held the proceeds for all the entrance fees to the convention, which totaled over $5 million.
Impressed by the action following Jack Rabble's arrest, Severin makes a sequel to the new Blue Falcon film with Garrison as the original Blue Falcon (who is the father of the new Blue Falcon) and Scooby-Doo as the original Dynomutt [which Stuffy describes as the best film ever].