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 for 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, but the Evil Entity kills Pericles and mutates his body into a squid-like monster. The Entity then consumes Brad and Judy and assumes control of the Kriegstaffelbots before consuming Mr. E and summoning other evil Anunnaki, who proceed to offer the townspeople for the Entity to consume. Scooby tries using the spear on the entity, but it shatters. The gang realizes that their friendship is the Heart of the Jaguar, and work together to get close to the sarcophagus. When Scooby destroys the sarcophagus, a vortex opens and sucks in and destroys the Entity, his minions, and much of the rest of Crystal Cove. The gang awakens to find themselves in a new version of Crystal Cove and Earth itself. After some strange encounters, Mystery Incorporated realizes that all the evil caused by the Entity has come undone, thereby changing history. The gang sets up a new Mystery Machine and travels off to Miskatonic University after receiving a message from Harlan Ellison, who is the new Mr. E and reveals he still remembers the previous timeline. The gang vows to solve each mystery they come across. As the gang drives away, they are watched by Nova, who says Scooby is the bravest dog that ever lived and thanks him and the gang.