Scooby-Doo! Mystery Incorporated is a reboot of the franchise of Scooby-Doo animated series. Fred, Daphne, Velma, Shaggy and Scooby-Doo make up the team of teenage mystery solvers who live in a small town called Crystal Cove. The town’s long history of strange disappearances, demon, phantom, ghost and monster sightings, and other paranormal activity. In addition to the traditional cases they always solve, the team finds itself being nudged into the uncovering of a dark secret that is hidden in the past of Crystal Cove. Standing in the way of their solving mysteries, is romance. Shaggy finds himself unable to put his new romance with Velma ahead of his longtime friendship with Scooby, while Daphne pines for Fred, who obliviously struggles to realize he shares her feelings too. Sometimes love is the greatest mystery.
The gang and original Mystery Incorporated stand before the Evil Entity. The Entity grabs Scooby-Doo, and mentions that he must die and be reborn as a vessel to its darkness. Scooby breaks free, but Pericles volunteers to be possessed by the being, to which the Entity agrees. Professor Pericles believes he has gained ultimate power (due to his growth in size and appearance), but the Evil Entity kills Pericles and mutates his body into a squid-like monster.
As the gang follows the original Mystery, Inc. through the caverns, they all approach the first gate to the cursed treasure. Professor Pericles knows the gang has been following them, as he calls them out to bring the Keys in order to open the gates. The gang realizes that the Keys and their scenarios seen in the dream world is how they all apply to the gates and the gates being opened. The gang decides to cooperate.
Once the gang returns to Crystal Cove, they discover that everyone in town has disappeared below ground. Later that day, after witnessing Mayor Nettles and Sheriff Stone vanish, the gang goes to Fred’s house to discuss the Planispheric Disk, Nibiru, the cursed treasure, and everything else associated with the mystery.
The gang goes south of the border in attempt to search for The Heart of the Jaguar.
When the Freak of Crystal Cove begins appearing in Scooby’s nightmares, the gang investigate what’s going on.