Dr. Phineus Phibes uses his new found nano-technology to clone himself into a mini-army of evil. Because Scooby eats too many super snacks, he becomes briefly immune to their effects. Without Scooby's super powers, Scoob and Shag are easy pray for Phibes and his gang of clones.
Phibes and Scooby and Shaggy decide to go on vacations but, as luck would have it, they book trips on the very same Mexican Cruise Line. They call a truce for the duration of the cruise. However, Phibes orders his agents to kill Shaggy and Scooby.
Phibes is a guest of Shaggy and Scooby after his evil clone kicks him out. However, Phibes can't stop himself of making prank phone calls to his doppelganger. Evil Phibes is enraged and decides to obliterate the world with one of Phibes' own devices.
Scooby and Shaggy settle into their favorite weekly ritual, super scary movie night. But little do they know, the evil Dr. Phineus Phibes is using them as guinea pigs for a new, super evil technology --- a high-tech DVD that projects scary "on screen" characters into reality as living breathing fiends.
Robi makes good on Scooby and Shaggy's request to become their personal super crime fighter agent trainer - in order to get them in super shape to fight super villains. Robi misunderstands a conversation he overheard between Scooby and Shaggy and decides to to leave and find a new life. Dr. Phibes captures Robi and it is up to Scooby and Shaggy to save him!
Dr. Phineus Phibes is convinced that the sole reason he is continually defeated by Scooby and Shaggy is that he is simply not smart enough. Phibes uses a nano-formula that makes him super smart. It is up to Scooby and Shaggy to use "dumb gas" to make Dr. Phibes stupid again.
When Dr. Phibes returns to the ranch that he grew up on, he makes giant, vicious animals like a hissing goat and a baaing bull and a giant turkey. With his new animal friends, he tries to take revenge over wrongs committed to him in his youth. Can Shaggy and Scooby stop him in time?