Shaggy and Scooby-Doo solve mysteries with the help of new nano-technology infused Scooby Snacks, which imbue the canine hero with special skills such as the ability to fly.
Shaggy's old dog called Zoinks arrives, who has been missing. Scooby and Zoinks do not get along and it turns out the dog was created by Phibes, to split Shaggy and Scooby up. So to make them hate each other more, Phibes creates Scooby's first master Groovy Don, Zoinks and Groovy Don try to destroy Shaggy and Scooby, but end up defeated by the Dynamic Duo.
Uncle Albert sends Shaggy and Scooby a message revealing that he has been working undercover for Phibes all along. Now Phibes too knows that there is a mole in his organization and plans to expose him. Now it is up to the duo to save their Uncle. But after locating him, they face an even bigger challenge as Phibes escapes and launches the Self Destruct Mechanism of the Lair. Finally Shaggy and Scooby send Phibes crashing and rescue Uncle Albert as well as the agents trapped inside the doomed lair, with Scooby using a "Hyper Speed Scooby Snack" given by Uncle Albert.
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