Mystery Inc. travels to San De Pedro, California for the "Mega Mondo Pop! Comic ConApalooza", so Shaggy Rogers and Scooby-Doo can enter a costume contest as their favorite comic book superheroes, the Blue Falcon and Dynomutt. There, they meet Jennifer Severin, a film producer in the midst of making a dark and gritty Blue Falcon film; the film's leading actor Brad Adams; Hank Prince, the owner of a comic book store that Shaggy frequents; his nephew Austin; Owen Garrison, the washed-up star of the original Blue Falcon television series; and Jack Rabble, a former BattleBots champion. When Shaggy and Scooby try to get Garrison's autograph, he instead rants to them about how Severin's studio plan to erase all trace of his series in preparation for the film. Amidst a screening for the film's trailer, Mr. Hyde, a villain from the Blue Falcon television series, emerges to terrorize the conventioneers.
As Mystery Inc. offers to investigate the attack, most of them consider Garrison to be the culprit. However, Shaggy and Scooby refuse to believe them and use surveillance footage to reveal Severin stands to gain increased publicity for her film from the incident while Adams dislikes his role in the film and hopes it will draw attention away from him so he can quit. Realizing Hyde's attacks were based on episodes of the Blue Falcon television series and that his next attack will involve mutagenic ooze capable of turning living creatures into monsters, Shaggy and Scooby flee into a storage room, where they find Hyde's lair before he chases them out and attacks the city with a harmless placebo of the ooze. Having been humiliated during the attack, San De Pedro's mayor, Ron Starlin, fires Mystery Inc. and has their access to the convention revoked.
Upon learning the Blue Falcon film premiere is being held at the local baseball stadium and deducing it will be Hyde's next target, Fred, Velma and Daphne gain Austin and Rabble's help in sneaking past the convention's security so they can infiltrate Hyde's lair. There, they learn that Hyde had been spying on the convention and stadium before witnessing a giant Hyde rampaging in the latter. Meanwhile, Shaggy and Scooby find themselves trapped in the stadium while searching for something to eat. Seeing Austin in danger, the duo rescue him before their friends arrive to defeat the giant Hyde and discover that it was actually a mech seemingly piloted by Garrison. Despite his pleas that someone knocked him out and framed him for the attack, Garrison is nearly arrested. However, Shaggy and Scooby see the real Hyde hijacking an armored car. Scooby foils the robbery, only for Hyde to soon gain the upper hand. Nonetheless, Garrison, donning his old Blue Falcon costume, joins Scooby in defeating the villain.
Hyde is then revealed to be Rabble, who confesses that he sought to take revenge on the convention after he was ousted from BattleBots when he used live missiles on one of his robots, leaving him to make money off of his convention appearances ever since. After forcing the premiere to be held at the stadium and planting Garrison in the mech, he used the attack to divert the armored car into a detour so he could make off with the five million dollars worth of the convention's entrance fees it had. As Rabble is taken into custody, Starlin arrives to congratulate and apologize to Mystery Inc. before re-granting them access to the convention.
Sometime later, an impressed Severin produces a sequel to her Blue Falcon film, with Garrison guest starring as the father of Adams' character and Scooby as Dynomutt.
