A robot disguised as a Nazi World War II soldier attacks Cassidy Williams at her radio station, eventually self-destructing as Cassidy fights back, taking the entire building with it. She explains to the gang that these robots have been attacking her for the past week. Robots continue to attack the gang as they investigate. When the gang realizes that the robots are coming from deep underwater, Daphne recruits two of her babysitting charges, Tom and Tub, and their seal (also named Scooby), to transport the gang in their submarine to the robots' spawning vats, in an area the kids call "The Midnight Zone". Shortly after submerging, the sub is attacked by a group of robots and damaged, and the gang stumble upon an underwater base and attempt to use it to repair the sub, only to discover that the base is the factory where the robots are constructed, run by Professor Pericles. In the end, Pericles escapes leaving the laboratory to self-destruct, possibly killing Cassidy Williams as the gang, Tom and Tub, and Scooby the Seal escape.

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. The Entity then assumes control of the Kriegstaffelbots and summons other evil Anunnaki, who proceed to offer the townspeople for the Entity to consume. When Scooby destroys the sarcophagus, the Entity is killed and a vortex sucks everything in, except for the gang, then explodes. The gang find themselves in a new version of Crystal Cove and Earth itself. After some strange encounters, Mystery Incorporated realizes that all the evil ever caused by the Entity has come undone, thereby changing history.