Anunnaki-possessed Nova reveals the history of the Evil Entity. During the previous Nibiru event, the Anunnaki 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 Anunnaki 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 Anunnaki 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 Anunnaki 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 Anunnaki. Suddenly, time freezes and Scooby-Doo receives a vision from Nova's Anunnaki, who tells him that the Heart of the Jaguar was never the spear at all. Much to Scooby-Doo's frustration, the Anunnaki'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 Anunnaki 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. Then, happens a huge galactic implosion followed by a bright light...
...and the gang happily sees themselves unharmed, the town around them seemingly untouched, and cheer their success. Before they could go to celebrate, Sheriff Bronson Stone and Janet Nettles appear before them, now apparently married with four kids (three sons and one daughter), who Daphne apparently promised to babysit, before leaving for the beach with their kids. The gang is perplexed by this and start really looking around, and notice some very drastic changes around Crystal Cove: First, they notice that the town sign now reads "The Sunniest Place on Earth"; second, another sign reveals that Danny Darrow is still alive (and is even the current dean of Darrow University) while Darrow Mansion is still above ground and has been declared a historical landmark.
The gang is even more perplexed by all these apparently sudden changes—Scooby even freaks out and screams, "What's going on?!" Velma responds with, "Scooby, I think that's exactly what we need to find out," and the gang splits up to investigate further.
Fred and Daphne go to Fred's house and discover not only Fred's (biological) parents, but Daphne's parents as well. As it would seem, in this new timeline, Fred was raised by both of his biological parents, who now have no interest in traps and apparently work as obstetricians (doctors that deliver babies). Also, it turns out that Daphne's are now supportive of her relationship with Fred, even to the point of helping to plan their wedding (revealing that Fred and Daphne are still engaged). And on another note, it turns out that Daphne's sisters (or at least the quadruplets) no longer hold the successful careers they had in the previous timeline and their parents are now more proud of Daphne than them.
Shaggy and Scooby arrive at Shaggy's home, discovering that Shaggy's the president of the chef's club and the winner of multiple cooking awards. Shaggy reminds his parents he's a slacker, but they don't buy it for a second. Watching television, Scooby and Shaggy discover that Destroido has been replaced with Creationex, that Ricky Owens, seen on a TV commercial for his company, is slender with a tiny beard, and he's married to Cassidy Williams, who helps run the place. Professor Pericles, their mascot, is still alive, unscarred, and friendly.
Velma arrives at her house, discovering she and Marcie Fleach (now her closest friend outside of the gang and later confirmed girlfriend) 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 soccer championship last night in the net. Fred Jones, Sr. is now the soccer coach and the school principal, but has never been mayor. Fred calls him "Mayor Dad" out of habit; to which Fred Jones, Sr. admits Fred's always been special to him. He gives Fred 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, and realize they're now in a better world with normal lives, but also a world without mysteries. The gang, who've devoted their lives to mystery solving, can no longer be detectives...
Upon playing the disc, Harlan Ellison appears, revealed to be Mr. E in this new universe. Harlan Ellison tells them he slipped through as well, and remembers everything. He now teaches sub-nuclear sciences at Miskatonic University, and has registered the gang in his class next semester. There's a lot of meddling and mysteries left, and they shouldn't miss it. Re-energized, the gang decide to start their trip immediately; Fred promises to solve every mystery along the way and stop at every food place and tourist attraction. They repaint the van in its original colors and prepare to leave. As they leave, Nova, seemingly still possessed by the Anunnaki, thanks Scooby Doo, calling him the bravest that ever lived. Scooby looks back one last time toward Nova and Crystal Cove, then faces forward, calling out "Scooby Dooby Doo!" as the gang drives off into the sunset.
- Mystery Incorporated (final appearance)
- Nova (final appearance)
- Fred Jones, Sr. (final appearance; dies in Nibiru, restored in post Nibiru)
- Harlan Ellison (final appearance)
- Evil Entity (final appearance; dies)
- Professor Pericles (final appearance; dies in Nibiru, restored as a good in post Nibiru)
- Brad Chiles (final appearance; dies in Nibiru, restored as good in post Nibiru)
- Judy Reeves (final appearance; dies in Nibiru, restored as good in post Nibiru)
- Mr. E (final appearance; dies in Nibiru, restored in post Nibiru)(redeemed)
- Kriegstaffebots (final appearance; destroyed)
- Hunters of Secrets (final appearance)(no lines)(flashback only)
- Spot (final appearance)(no lines)(flashback only)
- Alianza Misterio (final appearance)(no lines)(flashback only)
- El Fuchi (final appearance)(no lines)(flashback only)
- Fraternitas Mysterium (final appearance)(no lines)(flashback only)
- Benevolent Lodge of Mystery (final appearance)(no lines)(flashback only)
- Oswald P. Burlington (final appearance)(no lines)(flashback only)
- Marianne Blanchard (final appearance)(no lines)(flashback only)
- Scotty O'Rourke (final appearance)(no lines)(flashback only)
- Mr. Peaches (final appearance)(no lines)(flashback only)
- Abigail Gluck (final appearance)(no lines)(flashback only)
- Mystery Gang (final appearance)(no lines)(flashback only)
- Tiny (final appearance)(no lines)(flashback only)
- Mystery Fellowship (final appearance)(no lines)(flashback only)
- Brenda (final appearance; dies in Nibiru, restored in post Nibiru)(no lines)
- Photographer (final appearance; dies in Nibiru, restored in post Nibiru)(no lines)
- Mr. Baywosenthal (final appearance; dies in Nibiru, restored in post Nibiru)
- Miss Vampire Waitress (final appearance; dies in Nibiru, restored in post Nibiru)
- Sheriff Bronson Stone (final appearance; dies in Nibiru, restored in post Nibiru)
- Mayor Janet Nettles (final appearance; dies in Nibiru, restored in post Nibiru)
- Eastwood Stone (single appearance)(no lines)
- Norris Stone (single appearance)(no lines)
- Billy Jack Stone (single appearance)(no lines)
- Lynda Carter Stone (single appearance)(no lines)
- Danny Darrow (final appearance)(billboard)(cameo)
- Colton Rogers (final appearance)
- Paula Rogers (final appearance)
- Ricky Owens (final appearance)(cameo)
- Cassidy Williams (final appearance)(cameo)
- Barty Blake (final appearance)
- Nan Blake (final appearance)
- Daisy Blake (final appearance; dies in Nibiru, restored in post Nibiru)(no lines)(cameo)
- Dawn Blake (final appearance; dies in Nibiru, restored in post Nibiru)(no lines)(cameo)
- Delilah Blake (final appearance; dies in Nibiru, restored in post Nibiru)(no lines)(cameo)
- Dorothy Blake (final appearance; dies in Nibiru, restored in post Nibiru)(no lines)(cameo)
- Hotdog Water (final appearance; restored in post Nibbiru)
- Ethan (final appearance; dies in Nibiru, restored in post Nibiru)
- Gary (final appearance; dies in Nibiru, restored in post Nibiru)
- Ancient Egypt (flashback only)
- United States
- The Mystery Machine (restored in post Nibiru)
- The gang's reaction to defeating the Evil Entity and that they should celebrate mirrors what the gang did at the beginning of the first episode. They're even interrupted by Sheriff Stone who's now happy to see them instead of being mad at them for interfering.
- The scene of Daphne looking at her sisters is also mirrored from the first episode, although instead of being glamorous over-achievers with highly successful careers they are normal, unhappy under-achievers.
- Velma's flashback while explaining what happened includes the following unmaskings:
- Slime Mutant is Emmanuel Raffalo from Beware the Beast from Below.
- Aphrodite is Amanda Smythe from Where Walks Aphrodite.
- White Wizard is Mr. Wang from The Dragon's Secret.
- Nightfright is Argus Fentonpoof from Nightfright.
- Ghost Girl is Alice May from The Legend of Alice May.
- Phantom is Daniel Prezette from In Fear of the Phantom.
- Ghost of Dead Justice is Deputy Bucky from Dead Justice.
- Crybaby Clown is Baylor Hotner from The Night the Clown Cried II - Tears of Doom!.
- Hodag of Horror is Roberto from The Hodag of Horror.
- Mrs. Wyatt, under cloak, (who controlled the Fright Hound) from Howl of the Fright Hound.
- The Fiend is Dan Fluunk from Night Terrors.
- Mummy of Friar Serra is George Avocados from Theater of Doom.
- Zombie Rude Boy is himself from Dance of the Undead.
- Gluten Demon is Francilee Jackson from The Devouring.
- Dandy Highwayman is the librarian from Stand and Deliver.
- This episode is the last Scooby-Doo production to feature Casey Kasem, as well as his final acting role, before his death in 2014.
- This episode is one of the most darkest moments in the entire franchise as it features many deaths and destruction of the original timeline.
- In the scene where Shaggy, Scooby, Fred, Velma and Daphne are being chased by the Anunnaki, they ran in the same style as their original incarnations.
- New Crystal Cove timeline:
- The sign in front of Crystal Cove now reads: The Sunniest Place on Earth.
- Sheriff Bronson Stone and Janet Nettles are married and have three sons (Eastwood, Norris, and Billy) and one daughter (Lynda Carter).
- Darrow Mansion has become a historical museum. Danny Darrow is also alive and well, having become the dean of Darrow University.
- Fred is now living with his birth parents in the mansion where he was raised in by Mayor Dad. Pictures show that he has lived a happy childhood with them.
- Brad and Judy are obstetricians and not trap makers as they both deliver babies to the world.
- Daphne's parents approve of Fred and have planned their engagement.
- They are also more proud of Daphne than her older sisters who are now under-achievers.
- Daisy is not a medical doctor.
- Dawn is not a model.
- Dorothy is not a race car driver.
- Delilah is not in the Marine Corp.
- Shaggy is president of chef club and he has won many cooking awards. His parents are proud of him and don't believe he's a slacker.
- Destroido Corp. has become an environmentally friendly corporation called Creationex Corp.
- Instead of Mr. E, Ricky Owens is a well-fit man, and he's been married to Cassidy Williams, who appears to work with him.
- Professor Pericles is the happy, unscarred mascot of Creationex Corp.
- Velma and Marcie Fleach now work together in the Tri-State Olympiad of Science, which they always win. It was eventually confirmed by Tony Cervone, one of the creators of the series, that Marcie and Velma are also an official canon couple after the timeline reset.
- This also makes them the first confirmed gay couple in the franchise.
- Gary and Ethan are good friends with Fred, mostly because he is a great goalkeeper.
- Fred Jones, Sr. is now the soccer coach and principal. He sees the students as his children and is especially proud of Fred (Junior).
- Given Fred is still named after him in this timeline, it's highly likely he has a close friendship with Brad and Judy.
- The Mystery Machine is just a plain white van, until the gang paint it to the colors it was in the original timeline.
- Harlan Ellison is now Mr. E, possibly because of his last name.
- Nova is still possessed by the Anunnaki.
- Crystal Cove is probably larger in the new timeline, as Porto had no reason to blow up the old town of missionaries.
- The Horrible Herd and the Kriegstaffebots don't exist since Professor Pericles nor Abigail Gluck never had a reason to create them.
- Skipper Shelton would presumably have his nose.
- Some of the locations in Crystal Cove including the Crystal Cove Spook Museum, the Bloody Stake, K-Ghoul and other haunted themed areas don't exist as the town doesn't have any reason to build them.
- There were not disguises of monsters in Crystal Cove nor any mystery solving groups before Scooby-Doo's group.
- The scene where the gang throws each other the Heart of the Jaguar is similar to their theatrical live-action film incarnations throwing the control panel to each other in Scooby-Doo 2: Monsters Unleashed.
- The fact that the Evil Entity takes over Professor Pericles' army of Kriegstaffebots is similar to when the Amazing Krudsky takes control of the goblin minions of the Goblin King by getting rid of him with the goblin scepter in the direct-to-video film Scooby-Doo! and the Goblin King.
- Photos from Fred's new childhood has Brad wear clothing with a vertical blue strip on his top similar to what standard continuity Fred wore in the TV series What's New, Scooby-Doo?
- At the end of the episode, when Scooby and his friends are looking at the computer, they are making the poses their original incarnations made when reading the book in the Scooby-Doo, Where Are You! episode What a Night for a Knight.
- The gang in the live-action TV film Scooby-Doo! The Mystery Begins also painted their new van in a montage.
- A laugh track followed by applause is heard near the end of the episode when the gang is driving away.
- The conclusion to the series is also reflected in the background of the end credits. Gone is the dark purple background, replaced with the vibrant colours of the Mystery Machine, and also features the opening theme, indicating a whole new set of adventures.
- Casey Kasem and John O'Hurley are uncredited as Colton Rogers and Skipper Shelton, respectively.
- Disguises: None.
- The opening narration by Nova over a field of stars is an homage to the opening of David Lynch's Dune.
- Miskatonic University was created by horror novelist, H.P. Lovecraft in 1922.
Animation mistakes/technical glitches
- Delilah is shown to be the biggest of the Blake sisters, but in Beware the Beast from Below, she was shown to be the same size as the rest of her sisters.
Inconsistencies/continuity errors and/or goofs
- In the intro, the Nova Anunnaki misnames the Fraternitas Mysterium donkey as "Gordo" (which means "fat" in Spanish) instead of Porto.
- Angie and Dale are the only parents not seen in the new timeline. A part of the Spook Museum was visible, but it's still unclear what they do, since all the bad guys in masks never occurred in the new timeline. Then again, Crystal Cove still is an old town so maybe they give non-haunted tours.
- Ed Machine's place in the new timeline is also unclear.
- Fred is still called "Fred" by the inhabitants of the new timeline, even though Mayor Fred Jones never abducted him and changed his name to Fred Jones, Jr. It is possible that Fred could have been his original given name by coincidence, but presumably in this timeline his full name is Frederick Chiles (or Frederick Chiles-Reeves).
- It is unknown why the wedded Blake sister wasn't shown with the rest of the Blake sisters.
- Even though Fred Jones, Sr. isn't mayor anymore, he's still listed in the voice credits as such.
- Fred Jones, Sr. shouldn't be a resident of Crystal Cove in the new timeline. In All Fear the Freak, he states that the cursed treasure was the reason he moved in the first place. Without said cursed treasure (the Evil Entity) existing, he has no reason to be there.
- The Kriegstaffebots are listed as "Kriegstaffe Bots" in the voice credits.
In other languages
|Italian||I Misteri Non Finiscono Mai||The Mysteries Never End|
|Spanish (Latin America)||Liberados||Freed|
|Hungarian||Játszd újra, Scooby!||Play It Again, Scooby!|
|Greek||Η Ανατροπή της Πραγματικότητας||The Overturning of Reality|
- Scooby-Doo! Mystery Incorporated: Season Two, Part 2 - Spooky Stampede DVD set released by Warner Home Video on June 18, 2013.
- Scooby-Doo! Mystery Incorporated: The Complete Season 2 DVD set released by Warner Home Video on October 7, 2014.
- Scooby-Doo! Mystères associés: L'intégrale de la saison 2 (Scooby-Doo! Mystery Incorporated: The entirety of season 2) DVD set released by Warner Home Video on September 10, 2013.
Evil Entity: I bring oblivion to this world.
Scooby: It's the end!
Scooby: The heart is us. It's always been us.
Velma: I know why everything's different. We destroyed the Entity and by destroying it, it was as if it never existed. So everything it touched: all the evil, all of the curse, all of the losers in rubber masks and the dumb monster attractions, none of it ever happened. By destroying the Evil Entity, we created an entirely different timeline.
Harlan Ellison: I want you in my class next semester. I've already got you all admitted, even that weird dog. There's a lot of meddling to do and a lot mysteries that need solving. Don't miss it.
Fred Jones, Sr.: You've called Me a lot of things over the years. "Mr. Jones", "Coach Jones", "Principal Jones". But, definitely not "Mayor"... and never "Dad". I gotta say I like it. You know, since I never had kids of my own, I've always thought of the students here at my high school as all my kids. But you, Fred, you were always special. I've always been extra proud of you.
Fred: Hold the phone!
Nova: Thank-you, Scooby-Doo. You are the bravest dog that ever lived.
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