While in Tokyo for a martial arts tournament, Scooby, Shaggy and the rest of the Mystery Inc. gang, are confronted by the Black Samurai, an evil spirit who was vanquished in ancient Japan but has been mysteriously resurrected. In order to defeat the samurai, the gang will have to beat him in a treasure hunt across Asia, solving riddles and fighting a host of ninjas along the way.
Shaggy and Scooby win tickets to "WrestleMania" and convince the crew to go with them to WWE City. But this city harbors a spooky secret - a ghastly Ghost Bear holds the town in his terrifying grip! To protect the coveted WWE Championship Title, the gang gets help from WWE Superstars like John Cena, Triple H, Sin Cara, Brodus Clay, AJ Lee, The Miz and Kane.
A Man Crab attacks Crystal Cove beach during a volleyball tournament for Trickell's Triquid diet mixture. The gang must stop him and solve this mystery before the tournament's female players, who the Man Crab has taken a liking to, are put in danger. Meanwhile, Velma gets some relationship advice from Daphne.
There's a vampire loose in Crystal Cove, terrorizing the residents and stealing an odd assortment of loot. When the gang does some sniffing around, they discover an unlikely suspect… Daphne's MOTHER. Things are already strained within Mystery Inc., and with this latest blow, the gang is truly torn in half. Girls on one side, boys on the other.
With Mystery Inc. broken up, the gang decides to check out life after high school and spend a weekend at DARROW COLLEGE. But things don't go as planned when a creature called CHAR GAR GOTHAKON begins terrorizing the campus. Turns out this beast is a fictional character come to life. A creation of the author H.P. HATECRAFT who is a professor at the school.
Sick in bed right before the big Mystery Solvers Club State Finals, Scooby dreams about going to the competition and teaming up with fellow mystery-solver sidekicks Speed Buggy, Jabberjaw, Captain Caveman and The Funky Phantom to rescue their friends from the clutches of the demonic Lord Infernicus.
When Fred invites the gang on his and Daphne's second date, it pushes Daphne into the arms of Obnarb, the leader of an Orc Biker group called the Wild Brood who have come into town. When a break in at the armory happens and a dangerous weapon is stolen, the Wild Brood are the top suspects. It's up to the gang to solve this mystery, save the Wild Brood, and find the imposter Orc Biker.
When the gang goes on a quest to find out what happened to the original Mystery Incorporated group on their last case of the 75 year old disappearance of the Darrow Family and their mansion, they find themselves trapped in the underground Darrow Mansion, which has been booby trapped. Will the gang solve the mystery and escape with their lives?
When an exchange student named Mai Le comes to Crystal Cove, she draws the affection of Shaggy. A dinner party hosted by the Blake Family is interrupted by the Red Wizard warning to stay away from the Dragon's Heart which he has sworn to protect at all cost. Later, Mai Le and the gang to come under attack by a White Wizard who is after Mai Le's ring, and the Red Wizard comes to the gang's rescue, but he is too late to save the ring. The Red Wizard turns out to be Mr. Chen, the owner of Chen's Internet Cafe and Tea House. He reveals that with the White Wizard, now in possession of all four rings, is able to open the Jade Dragon's Heart, which is a priceless ruby. Will the gang solve the mystery or is everything not as it seems?
Scooby and Shaggy win an essay contest to have dinner with Vincent Van Ghoul. They go to his mansion and are attacked by a monster who calls himself Nightfright. Shaggy calls the gang and the gang rushes over. The are chased by Nightfright and go into a room and lock the door. Fred makes a trap and asks Vincent to lure the monster into it. Finally, they catch Nightfright in Fred's trap. The end of the episode shows them eating dinner, Daphne devouring everything in sight because she has not eaten for hours.
When Mayor Jones buys online an ancient Persian temple, in order to boost business in Crystal Cove's amusement Park, "Creepy Spooky Terror Land", he never thought that that temple would come with a Manticore, a vicious mythological animal, who is been eating the park's visitors. Having no other option, he asks Fred and the gang to help him capture the beast, and while they do it, he does some snooping around, regarding the mysterious puzzle piece that the gang found in Darrow Mansion.
When Fred's favorite adventurer, Dr. Rick Spartan, starts teaching biology at the Crystal Cove's High School, the gang gets to meet him. Fred tells him that the gang has also been into some terrifying experiences, Spartan immediately invites them to have dinner at his place, where he promises to show them his latest trophy, the cursed Shrunken Head of Squar Gringot. But when its headless body appears and threatens to pursue the professor until the end of his days for plundering its tomb, the gang must find out a way to break the curse.
The gang finally follows the trail to find the hidden treasure, but they didn't think The Freak would go after them. On the other hand, many truths are revealed, including the goal of Professor Pericles and the true identity of Fred's parents. And as if that were not enough, the gang faces a big problem when the parents get angry due to the behavior of their sons. And just when the mystery of the town is at its highest level, does this mean the end of the gang or the beginning of a new problem?
As Shaggy and Scooby are running away from a monster, Olympic Games organizer Diane watches Shaggy and Scooby's amazing running ability and asks them to join the 2012 World Invitational games (a parody of the 2012 Summer Olympics) in London. Shaggy accepts the offer, while Scooby is unable to join (because he is not human). Instead, Scooby-Doo becomes Shaggy's coach. The gang is flown on an all-expenses-paid trip to London so Shaggy can participate in the games. When they arrive, Daphne and Velma become interested in Steve Looker, an Olympic pole vaulter, causing Fred to want to become a pole vaulter in the games. The gang then goes to their hotel room, and Scooby hears a loud stomping noise outside while he is watching a Gladiatorsaurus marathon on TV. Shaggy and Scooby take a peek at what is going on, and find that a 2000-year-old Olympic statue has come to life and is terrorizing the city.
A Graveyard Ghoul attacks in the middle of Mayor Nettles' Horror Movie Night, forcing the gang to investigate. However, Fred and Shaggy are smitten with three beautiful girls who have just immigrated into Crystal Cove, and Daphne has eaten some of their mother's homemade chocolate and become addicted, leaving Velma and Scooby alone to solve the mystery. Eventually, they are forced to turn to Sheriff Stone for help. Meanwhile, Mr. E teams back up with Professor Pericles in search of what he calls "the Treasure".
A family vacationing in the Burlington Library (the same family which was vacationing in the "The Creeping Creatures") is attacked by a wolf creature and scared off. Later, a landslide forces the gang to abandon their ski vacation and detours them to the same library, where they are greeted by its caretaker, Dan Fluunk, who explains to the gang the history behind the mansion, including that its builder and namesake had a fascination with groups of four people and an animal. Soon, strange things begin happening to the gang as their stay in the mansion progresses. Eventually, their experiences are revealed to be hallucinations brought on by burning of a special kind of wood. Meanwhile, Cassidy Williams continues her search for the truth behind why what is happening to the gang now has happened to other gangs in the past -- including the Darrow family.
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.
A bear-like creature attacks Mayor Nettles and Sheriff Stone in the Crystal Cove woods near Destroido. They turn to the gang for help, explaining that the creature is called the Scarebear and has been stalking the grounds near the Destroido company for weeks. The gang finds out that the Destroido company has allowed toxic lithium to spill into the woods, which has resulted in the mutations of inhabitant plants and creatures including the Scarebear. Meanwhile, Mr. E and Professor Pericles have recruited Brad and Judy to help them find the gang's pieces of the Planispheric Disk, and have resorted to drastic measures to get the gang out of the way.
A teenager vandalising a neighborhood is attacked by a creature calling itself "Krampus," leaving his hair snow-white with fear. Three more kids are attacked as the gang meets Mayor Nettles and Sheriff Stone at the roller rink and arcade. Realizing that Krampus attacks "bad kids" such as the aforementioned teenager, the gang turn to the imprisoned Mary-Ann Gleardon for help only to have Krampus attack and kidnap her from prison. In the end, it's revealed that the gang had enrolled the forces of Hot Dog Water, Jason Wyatt, Mary-Ann Gleardon, Ex-Mayor Fred Jones Sr., and Charlie the Robot (from the Haunted Museum exhibition) in an elaborate scheme to steal the original Mystery Incorporated's pieces of the Planispheric Disk. After the gang reassembles the disk, the eyes of the Crystal Coffin glow and it mutters "Nibiru."
Five years ago, a gigantic dragon robot attacks the Quest Industries, then promptly vanishes, leaving the security guard's dog unconscious; Dr. Benton Quest works to revive the dog. In the present day, the same robot attacks the gang at city hall as they begin their investigation into the purpose of the Planispheric Disk; however, the gang is saved by Blue Falcon and Dynomutt, who explain that they have been tracking the robot for years. Velma rudely tells the heroes that Crystal Cove is their turf, and Blue Falcon offers the gang to tag along. Together, they find that Quest Industries has been sold to Destroido. Upon investigation, the dragon-robot attacks, intending to kidnap Dynomutt, only to make off with Scooby-Doo instead. Using a tracking device located on Falcon's belt, the gang and Dynomutt are able to locate Dr. Zin's lair and save their friends.
A gluttonous monster attacks Francilee Jackson on her cooking show. As the gang attempts to eat dinner together, the restaurant is crashed by Rick Spartan and Cachinga, who are on the hunt for the monster. The monster attacks various locations around Crystal Cove, including various restaurants and the museum where Velma's mom works. Meanwhile, Professor Pericles has gone crazy, leaving Mr. E to attempt to seek the treasure without him. Brad and Judy tell Pericles of E's mutiny, and Pericles uses venom injections to force Mr. E to work for him.
As the gang investigates a haunted house, a man resembling Fred pulls Fred through a mirror and takes him to a world where the Planispheric Disk destroyed all of Crystal Cove. Meanwhile, in the real world, Fred begins acting strangely. The real Fred manages to tell the gang that the Fred in their world is fake, having discovered so when a fake Daphne in the "mirror world" gave herself away. When the ruse is discovered, Professor Pericles uses the Kriegstaffelbots to threaten Daphne in order for the Planispheric Disk to be surrendered to him. When Professor Pericles gets the Planispheric Disk, he makes plans to free his "master."
When a monstrous version of the Freak of Crystal Cove begins appearing in Scooby's nightmares, the gang decides to investigate what's going on. They seek the help of the reclusive hypnotist Professor Horatio Kharon (author of the book Velma has been reading), who has also been seeing the Freak within his dreams as well as appearing in Scooby's. After being hypnotized to enter the dream world, the gang is chased by the Monstrous Freak throughout the dimension. They soon discover the evil entity that was trapped with the cursed treasure, and how previous mystery groups and the people affiliated with the treasure have been manipulated by the entity. The being speaking through Nova tells Mystery Incorporated that they must find the Heart of the Jaguar in order to destroy the evil entity sealed within the crystal sarcophagus.
The gang, accompanied by Velma's mom, goes to Yucatán in an attempt to search for the Heart of the Jaguar after Angie's old friend, Professor Enrique Andelusossa, is "consumed by the jungle" near the Temple of the Hunters (the burial site of the Hunters of Secrets where the Heart of the Jaguar is kept). Upon arriving in Yucatán, the gang visits Professor Enrique's antique shop, where they are greeted by his angry wife, who says Mrs. Dinkley is to blame for his disappearance. After hours, the gang returns to the store, only to be attacked by the Mayan Priestess who warns them away from the temple. The gang ignores her threat and travels into the jungle to find the temple. Due to Fred's master trap skills, Mystery Incorporated overcomes the temple's diabolical traps and discovers the Heart of the Jaguar in the tomb. The Priestess attacks, but fails and is captured by the traps in the temple, which she triggered. Afterwards, a woman who had been spying on the gang appears, but is revealed as working with Mayor Nettles.
Once the gang returns to Crystal Cove, they find out that everyone in town has disappeared below ground. Later that day, after witnessing Mayor Nettles and Sheriff Stone vanish, the gang goes to Fred's house to discuss the Planispheric Disc, Nibiru, the cursed treasure, and an upcoming planetary alignment. After the interruption of Kriegstaffelbots, the gang sets off beneath Crystal Cove, and discovers everyone in town working for Professor Pericles and the rest of the original Mystery Incorporated. After hearing a conversation between the old Mystery, Inc., the gang is convinced they have gone crazy, and devise a tactical plan to bust everyone out and shut down the operation. Shaggy and Scooby go undercover as Kriegstaffelbots, while Fred and the girls attack in a suited-up Mystery Machine. After the word is spread, Sheriff Stone has everyone rebel against the Kriegstaffelbots and go on a riot. Soon, the Kriegstaffelbots stop Fred, Velma, and Daphne in their tracks, forcing them to blow up the Mystery Machine (in which everyone thought they were). After all is resolved and the doorway is opened to the cursed treasure, the gang gears up with the relics and follows the original Mystery Incorporated into the caverns.
As the gang follows the original Mystery, Inc. through the caverns, they all approach the first gate to the cursed treasure. Professor Pericles knows the gang has been following them, as he calls them out to bring the Keys in order to open the gates. The gang realizes that the Keys and their scenarios seen in the dream world is how they all apply to the gates and the gates being opened. The gang decides to cooperate, after Pericles reveals that they have Hot Dog Water, and opens the first gate. Thanks to Hot Dog Water, the gang enters the first gate; however, Hot Dog Water is killed by the Kriegstaffelbots nearly straight afterwards. The gang arrives at the second gate, and opens it using the mortar bowl. They enter a mysterious rock dimension, where they are greeted and chased by a Rock Monster. After the monster's failure, the gang comes before the third gate, which is opened using the conquistador's helmet. The gate then releases water trapped behind and turns into a boat, allowing Scooby and the gang to escape and become stranded at sea. After learning that the next gate is below the water, the gang comes upon the final gate, which is opened using the flintlock. The gang enters the dimension, which is teeming with lava, and come upon the crystal sarcophagus and cursed treasure, realizing that they are beneath Crystal Cove. The Evil Entity sealed within tries to manipulate the gang into opening the sarcophagus to free it, but the gang realizes the words the being is speaking aren't true. Suddenly, Pericles and the original Mystery Incorporated arrive and Pericles opens the sarcophagus, releasing the Evil Entity.
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. The gang sets up a new Mystery Machine and travels off to their new destination after receiving a message from Harlan Ellison, vowing to solve each mystery they come across. As the gang drives away, they are watched by Nova, who says Scooby is the bravest dog that ever lived and thanks him and the gang.