- "When the Cicada Calls" reveals that the guy who has been helping Mr. E is the head of a company that puts landfill in their snack products. This can be verified through the voice credits here.
- "The Siren's Song": Angel and Cassidy are the same person.
- "Menace of the Manticore" Confirms both of the above reveals and shows that Angel is spying on the gang for Mr. E, shows Mayor Jones is after something, and reveals the face and identity of Mr. E.
- "A Haunting in Crystal Cove": We finally get some information about Fred's Missing Mom. Mayor Jones turns out to have been hoarding a piece of the disc which he stole from Professor Pericles. The Monster of the Week turns out to BE Professor Pericles who has hijacked Fred's traps to use against him and his father. The gang FAILS to catch him since he pulls a booby trap on them shortly after the unmasking and makes off with the disk. Phew...
- "All Fear the Freak": Mayor Jones was the Freak that drove off the original Mystery Incorporated, and made them leave town afterwards; he also convinced Pericles to betray the original Mystery Incorporated. Freddie is actually the son of Brad and Judy. And the whole gang is broken up as Pericles gets away with both known pieces of the Disk.
- "The Night the Clown Cried" Daphne's moved on from Fred, Fred's plan fails, The Bad Guy Wins, and the town is up in flames and fireworks. And this is just the premiere!
- "Web of the Dreamweaver" has Fred's real parents—Brad Chiles and Judy Reeves—show up at the end.
- Then in "Hodag of Horror", they're nowhere to be found after the Hodag dognaps their pet Nova, only for them to show up at the end with Cassidy and Mr. E (Ricky). They've all been assembled for a discussion on the disc pieces by Professor Pericles.
- "The Gathering Gloom": Mr. E teams up with Professor Pericles.
- "The Midnight Zone": Cassidy dies.
- "Wrath of the Krampus" has the gang working to solve a typical mystery... only at the end, it's revealed THEY set it up in the first place to distract the original Mystery Incorporated, with the help of five former villains (including Scooby-Doo, Where Are You!'s Charlie the robot.) Their real intention was to get the last three pieces of the Planispheric Disk from the original Mystery Incorporated, assembling the full disk at last.
- And then in "Theater of the Doomed", the gang discovers that there was yet another foursome of mystery solvers with an animal companion back during the earliest days of Crystal Cove, and like the first Mystery Incorporated, the animal companion betrayed them. I really wouldn't want to be Scooby at this point.
- "Stand and Deliver": The nature of the Nibiru monster is revealed as an evil interdimentional being.
- "The Man in the Mirror": Pericles steals the Planespheric Disk.
- "Nightmare in Red": Mystery Inc. has been manipulated all this time by the entity, who plans on using them to release him. Shaken by all this, they resolve to get a spear that will destroy the entity for good. On the other hand, Fred and ex-Mayor Jones reconcile.
- "Gates of Gloom": Pericles kidnapped the populace of Crystal Cove to dig for the gate to the entity. The gang springs them in an uprising, but Pericles opens the gate, and the gang resolve to stop him first with all the remaining keys and treasures they have left. Oh, and Hot Dog Water is dead.
- "Come Undone": The Entity awakens and kills everyone bar the gang as well as destroying Crystal Cove, the gang kills the Entity with the Power of Friendship, which leads to a Reset Button Ending/Cosmic Retcon in which the universe restarts. The new universe is one without the corrupting influence of the Entity, meaning that just about everyone in Crystal Cove is happy and there were never any mysteries. The gang goes on a cross-country trip to Miskatonic University after Harlan Ellison invites them there and reveals that there are still more mysteries to solve, with the implication that the show is a Stealth Prequel to Scooby-Doo, Where Are You!.
Wham Episode / Scooby-Doo! Mystery Incorporated