When Mystery, Inc. are guests of honor at the grand opening of the Coolsville Museum of Criminology, a masked villain shows up and creates havoc before stealing the costumes of the gang's most notorious villains...Could it be that their nemesis, mad scientist Jonathan Jacobo has returned and is trying to recreate their deadliest foes?

The Mystery Inc. gang have gone their separate ways and have been apart for two years, until they each receive an invitation to Spooky Island. Not knowing that the others have also been invited, they show up and discover an amusement park that affects young visitors in very strange ways.