I know why everything's different. We destroyed the Entity and by destroying it, it was as if it never existed. So everything is touched: all the evil, all of the curse, all of the losers in rubber mask and dumb monster abstractions, none of it ever happened. By destroying the Evil Entity, we've created a totally different timeline.
- 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.
- This is both the season two finale and the series finale of Scooby-Doo! Mystery Incorporated.
- 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 cr s. 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.
- 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 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.
- 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 (Jr.).
- 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 higher because in the new timeline, Porto had no reason to blow up the old town of missionaries.
- The Horrible Herd and the Kristoffabots don't exist since Professor Pericles nor Abigail Gluck never had a reason to create them.
- Skipper Shelton would presumably have his nose.
- 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 the one in Scooby-Doo 2: Monsters Unleashed with the control panel.
- 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 sceptre in Scooby-Doo! and the Goblin King.
- Velma's flashback while explaining what happened includes photos from Wrath of the Krampus, Scarebear and A Haunting in Crystal Cove, as well as the unmaskings of the Slime Mutant (Professor Raffalo), Aphrodite (Amanda Smythe), the White Wizard (Mr. Wang), Nightfright (Argus Fentonpoof), the Ghost Girl (Alice May), the Phantom (Daniel Prezette), the Ghost of Dead Justice (Deputy Bucky), Crybaby Clown (Baylor Hotner), the Hodag of Horror (Roberto), Mrs. Wyatt in the cloak, (controlling the Fright Hound), the Fiend (Dan Fluunk), the Mummy of Friar Serra (George Avocados), Rude Boy (himself) and the Gluten Demon (Francilee Jackson).
- Disguises: None.
- The opening narration by Nova over a field of stars is an homage to the opening of David Lynch's Dune.
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.