Shaggy inherits "Like a Billion Dollars" from his Uncle Albert; an eccentric scientist and inventor who has suddenly disappeared. Scooby-Doo and Shaggy move into Uncle Albert's mansion and go from living "paw to mouth" to having everything and anything they've ever wanted! Just when Scoob and Shag kick back to enjoy their new digs, they stumble upon Uncle Albert's secret lab, where they discover the following that Uncle Albert is actually hiding from a sinister villain named Dr. Phineus Phibes, that Phibes is after a secret formula that Uncle Albert recently invented and finally that the formula is hidden inside a NEW IMPROVED formula for SCOOBY SNACKS! After being dragged off by Dr. Phibes' Agents to his secret submarine lair, Scooby and Shaggy use the NEW SUPER SCOOBY SNACKS to make Scooby INVISIBLE, scare off Phibes' agents and get away. Scooby and Shaggy vow to work on their own until they bring down Phibes.

Scooby and Shaggy are alerted through Uncle Albert and Robi that Dr. Phineus Phibes is planning to use a heat ray to melt a massive glacier on Mount Zeryodelwietzen (the white yodeler) in Switzerland. Phibes plan is to get revenge on a group of scientists who once mocked him, and who are holding a global warming conference at the base of the glacier. Scooby and Shaggy fly to Switzerland in the Mystery-Jet, discover that Phibes is hiding in his cloud ship lair above the glacier and, after defeating his pigtailed Swiss assassins (Misty Swiss and her evil bimbo dog Carla), derail Phibes' plan and save the day. In the meantime, they also find time to re-carve the face of the glacier to look exactly like Scooby.

When Dr. Phineus Phibes decides to kidnap three world famous inventors from a high society country club awards ceremony -- Scooby and Shaggy put on their fanciest duds and crash the event. After offending everyone they encounter and starting a massive food fight, Scoob and Shag hit the links with their Mystery-Golf Cart and cause even more mayhem, before eventually getting kidnapped in an ice cream truck. Just as Phibes' agents are about to make off with the inventors, Scoob and Shag charge to the rescue. And with the help of a Scooby Snack that makes Scoob magnetic, they disarm the villains (one of whom fancies himself a ninja) and rescue the inventors.

Robi goes on the blink during the eve of an all-important mansion housewarming party, forcing Scooby and Shaggy to replace him with a new robot butler. Little do they know, the new "ro-butler" is actually a terminator-like annihilator-bot built by Dr. Phineus Phibes. After Scooby and Shaggy repeatedly frustrate the robot, Dr. Phibes gives the order for a full-on assault. By using a Scooby Snack that gives Scooby transforming battle-bot capabilities -- and with the help of Robi, who has been sequestered in a closet-- Scooby and Shaggy fight back. In the end, they save themselves from being expelled from the neighborhood; manage to make Mr. Havansimp, the President of the housing association, a foot taller; and, in the meantime, throw the best party in history.

Scooby and Shaggy intercept KEVIN, an evil, artificially intelligent computer virus -- before Dr. Phibes can use him to infect the computer systems of the nation's weapons defense systems. Once Kevin takes up residence in the "Smart House" computer system of the mansion, he sets off on his own personal mission of world conquest. Just as Kevin is about to destroy Scooby and Shag and move on to rename the world "Kevin-Ville," Scooby miniaturizes himself with a Scooby Snack and, with the help of Shaggy and two of Dr. Phibes' own agents, manages to shut Kevin down and eventually upload an irritating but powerless version of him back into Dr. Phibes' own computer system.

From his spaceship lair, Dr. Phineus Phibes attempts to create an electrical storm that will forever envelop Earth. He also decides that the epicenter of the storm is going to be Scooby and Shaggy's mansion. Overcoming his intense (and very dog-appropriate) fear of lightning, Scoob travels with Shag to take on Phibes. With the help of a Super Speed Scooby Snack (and Phibes' own men, who believe Scooby and Shaggy are wise, avenging aliens) our heroes save the day -- and Earth with it!