Nova

The Annunaki possessed Nova reveals the history of the Evil Entity. During the previous Nibiru event, the Annunaki descended to Earth to aid the development of humanity, only for some to rebel and attempt to use the humans for their own ends. The good Annunaki halted their attempts, sealing away the most evil of the rebels inside a crystal sarcophagus. However, the Evil Entity's machinations have finally led to its release, and it will only grow more powerful with every second it spends in the physical world. Nova's Annunaki declares that the only hope for the world's survival now rests with Scooby-Doo and his friends...

In the lava-filled cavern beneath Crystal Cove, the gang and the old Mystery Inc. (minus Cassidy Williams) stand before the newly-freed Evil Entity. Grabbing Scooby-Doo, the Entity declares that he must be devoured and reborn as a vessel to its darkness. Scooby breaks free, but Pericles volunteers to be possessed by the being, believing that he will gain unlimited power.

Agreeing to this deal, the Entity seizes Pericles and pours its essence into his body, causing him to grow into a dark green giant. Gloating about his newfound power, Pericles prepares to destroy the gang, but the Evil Entity proceeds to subdue his consciousness and mutate the parrot's body into a massive squid-like monster with horns. Brad Chiles and Judy Reeves (after having plastic surgery) offer themselves as servants to the Entity, but the monster instead consumes them to increase its own strength. It then assumes control of the Kriegstaffebots, sending them to capture the gang and Mr. E.

The remaining humans flee, but Scooby-Doo stays behind, intent on destroying the Evil Entity with the Heart of the Jaguar. Unfortunately, the spearhead shatters upon contact with the Entity's head, forcing Scooby to flee before the Entity consumes him. Meanwhile, the gang manages to destroy five of the Kriegstaffebots -- Shaggy knocks two of them into a lava pit, while Fred and Velma disable three more with a barrage of gems fired from an old cannon. The last Kriegstaffebot manages to ambush the gang and lead them back towards the Entity for devouring, but Mr. E leaps from a nearby pile of treasure and decapitates it with a sword.

Mr. E tries to buy the gang time to flee, but the Evil Entity almost immediately grabs him with its tentacles. The gang tries to pull him loose, but Mr. E tells Velma that it's too late for him before being devoured. The Entity turns its attention towards the gang once again, but its tentacles are blocked by a shield of blue energy that appears around them. The evil Annunaki decides to instead turn its attention towards Crystal Cove, causing lava to erupt beneath the city. As people panic and the city's main sign burns (mirroring Scooby-Doo's vision in an earlier episode), the Evil Entity opens the Crystal Sarcophagus and releases an army of minions. The gang flees as the minions swarm into the town, bringing townspeople to the Entity for devouring.

As they continue to evade the Entity's legion of monsters, the Gang wonders why the Heart of the Jaguar proved useless against the evil Annunaki. Suddenly, Scooby-Doo receives a vision from Nova's Annunaki, who tells him that the Heart of the Jaguar was never the spear at all. Much to Scooby-Doo's frustration, the Annunaki's only hint to the true identity of the Heart is a cryptic statement: "You will know. You will see. You will feel."

The gang's flight from the evil Annunaki minions takes them back to the Evil Entity, where they bear witness to the devouring of the citizens of Crystal Cove. Spotting the gang in the middle of its feast, the Entity tries to consume them once again, only to be thwarted by the same barrier that protected them before. Recalling Nova's words, Scooby has an epiphany: the true "Heart of the Jaguar" is the power of friendship and love, embodied by the bonds between himself and his friends. Velma also realizes that the Evil Entity's weak point is the crystal sarcophagus, which it has converted into a portal to an alternate dimension to further empower itself.

With that, the gang grabs the remains of the Heart of the Jaguar spear and races towards the sarcophagus. The Evil Entity's minions attempt to stop them, but each member of the gang manages to toss the staff to the next before being subdued. With a final leaping kick, Scooby-Doo launches the staff into the crystal sarcophagus, opening up a vortex which begins to suck everything into it, except for the gang.

After a galaxy implosion and a bright light, the gang are happy to see the town untouched and cheer in their success. Before they could go to celebrate, Sheriff Bronson Stone and Janet Nettles appeared with four kids (one girl, and three boys) revealing to be their children. Daphne was said to have promised to babysit their kids at before they leave to the beach. The gang is perplexed and get even more baffled when the Crystal Cove sign reads "The Sunniest Place on Earth", and another features Danny Darrow, alive, and now exhibits the Darrow Mansion. They decide to investigate even further.

Fred and Daphne arrive at Fred's house, with pictures Brad Chiles and Judy Reeves living it with childhood pictures on the wall and new furniture. His parents are also now both obstetricians, not caring about traps. Daphne's parents are also there and are planning a wedding for Fred and Daphne seeing that they're almost 18 and by time they tied the knot and wished they could find more perfect manhood like Fred for Daphne's unachieving sisters.

Shaggy and Scooby arrive at his mansion, where it relieves that Shaggy is the president of the chef's club and the winner of multiple cooking awards. Shaggy reminds them he's a slacker, but his parents don't buy that story for a second. Scooby and Shaggy watch on tv that Destroido has been replaced with Creationex, and that Ricky Owens, seen on a TV commercial for his company, is slender and his beard is tiny and only under his chin. He is married to Cassidy Williams, who helps run the place and Professor Pericles is still alive as their mascot and pet, without the scar as he looked in the yearbook photo and friendly personality.

Velma arrives at her house and finds out that she and Marcie Fleach are a team and win every year at the Tri-state Olympiad of Science. Finally, Velma understands what's happening

Fred arrives on the school field, congratulated by Gary and Ethan for winning them the championship last night in the net. Fred Jones, Sr. is now the coach and princible, and never has been mayor. Fred calls him "Mayor Dad" out of habit, and Fred Jones, Sr. tells him that he had always been special to him and gives him a disk from Miskatonic University, with the Mr. E seal.

The gang learns that after the Evil Entity was destroyed, a new timeline was created, thus leading them to realize they're now in a better world with normal lives. Sadly, they also created a world without mysteries and since they devote their lives to mystery solving, they are depressed cause they can't be detectives anymore.

When played, Harlan Ellison appears, revealed to be Mr. E in this universe. Harlan Ellison tells them that he slipped through as well, and remembers everything. He now teaches sub-nuclear sciences at Miskatonic University, and that he has registered them in his class next semester. He tells them there's alot of meddling and mysteries that need solving and tells them not to miss just as the disc ends. The gang is motivated by this and they decided to drive right now and Fred promises to solve every mystery on the way, and to stop at every food place and other places. They paint the van to look like it did before and get ready to leave. As they left, Nova, seemingly still possessed by the Anunnaki, thanks Scooby Doo and that he is the bravest that ever lived. Scooby looks back one last time on Nova and Crystal Cove, then faces forward, as he calls out: "Scooby Dooby Doo!", as the gang drives off into the sunset.