Scooby and Shaggy travel into the desert to discover that Dr. Phineus Phibes has built a giant, weaponized robot in his image. Phibes' plan is to merge with the robot and become one with it, making himself all powerful and immortal.
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.
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.