In Coolsville, Ohio, four teenagers are involved in a fight on the school bus, which causes the bus to crash into a flagpole, which falls on Vice Principal Grimes' 2007 Ford Mustang, smashing its windshield. Because of the fight on the bus and the damage to Grimes' car, the teenagers are sent to the library for detention. Norville "Shaggy" Rogers is a clumsy, geeky outcast, who tried to smuggle his dog Scooby-Doo onto the bus; Fred Jones is quarterback of the football team; Velma Dinkley is a science nerd; and Daphne Blake is in the drama club and very wealthy. They bond somewhat over a shared interest in mysteries, but quickly get on each other's nerves. Two ghosts suddenly appear and chase them to the gym where a pep rally is going on. A third ghost, The Specter appears, causing the lights in the building to flicker. He starts telling everyone to leave. The stamp-collecting Principal Deedle decides to close the school, but Vice Principal Grimes deems it a prank and suspends the quartet as he refuses to believe that there are ghosts in the school.
The gang tries to clear their names by investigating the ghosts at the school, which leads to Grimes expelling them and threatening to have them arrested if they're caught sneaking into the school again. Further investigation, in disguise at the school, makes them think Grimes is their prime suspect. Searching at night at Grimes' house leads them to information about a time capsule. The ghosts attack again, and the teens are knocked out. The Specter, keeping Scooby and Grimes as prisoners, forces the gang to search underground for the time capsule. Unable to find the capsule, they trick the Specter into coming down to carry the capsule out of the hole, but the plan backfires when they try to lock him up in a flooded room, and the Specter acquires the capsule.
Stealing the capsule back, the gang uses a book of spells to banish the ghosts. Scooby manages to break free of his restraints and arrives just in time to subdue the Specter, who turns out to be Principal Deedle. The principal reveals that a stamp misprint was hidden within the time capsule, something that would have been worth a fortune. The time capsule was meant to be opened when the school first opened, but a flood hit the town that day. Deedle being determined to claim the misprint in the time capsule used the spell book to summon the ghosts to scare everyone away so he as the Specter can open the time capsule himself. As the exposed Deedle is fired from his job and is sent to prison for his crimes, the group is publicly congratulated (and un-expelled) by Grimes (who becomes the new Principal) who also apologizes to the gang for falsely accusing them. In the film's ending, the group decide to stay together and solve mysteries, and they head off to "investigate some strange goings-on at the Coolsville museum", a hint to the very first episode of Scooby Doo, and their very first case, The Black Knight Ghost.
- The DigiDestined and their Digimon (Digimon Tamers) will be guest stars in the film.
- Tino and his friends will meet Shaggy, Fred, Velma, Daphne and Scooby. Later they meet Takato and the rest of the Digimon Tamers for the very first time in this film.
- Bowser, Bowser Jr., Mistress 9 and Ranamon will made their first appearance in the film.