List of Scooby-Doo! Mystery Incorporated episodes

A slime mutant that lives underneath Crystal Cove is cocooning anyone who gets in its way. Despite being warned not to continue investigating by their parents and authority figures, the gang attempts to solve the mystery. Meanwhile, Velma is trying to get Shaggy to be more intimate in their secret relationship. Daphne also keeps hinting her romantic feelings towards Fred who is oblivious to almost everything apart from solving mysteries and building traps. After solving the mystery the gang comes into contact with a mysterious man who refers to himself as "Mr. E" and remarks that they have uncovered "a truth that should have remained buried" and that "the real mystery has just begun".

Overarching Mystery Clues: A locket shaped like a magnifying glass found in the Crystal Cove caves and a call from Mr. E.
Villain: The Slime Mutant/Professor Emmanuel Raffalo

The gang receives a package from Mr. E that contains a new handbag made in Gatorsburg. They travel to Gatorsburg to investigate the mystery of the Gator People. Velma becomes angry with Shaggy for not telling Scooby about their relationship. After being forced to spend the night at a local hotel the gang ultimately solves the mystery. Afterward, they find a note from Mr. E. in the Mystery Machine telling them that this mystery "is only one piece of the puzzle".

Crystal Cove is being terrorized by a mysterious Ghost Truck that has been running people off the highways. Meanwhile, Fred is helping his dad who is running for reelection as mayor and Daphne's parents are trying to set her up with the young heir to a ladder company. As all of this is happening, numerous crystal doorknobs are stolen from all around Crystal Cove. With the help of Mr. E. the gang solves the mystery.

During a volleyball tournament down at the Crystal Cove beach a giant crab beast attacks those who are present. The beast wants to ruin Trickles's volleyball tournament for taking credit of the beast's invention. The beast kidnaps Daphne which places Fred in a state of total shock rendering him unable to say anything that doesn't relate to her. The gang receives an old newspaper article from Mr. E about four kids who disappeared in the Crystal Cove caves many years prior. The gang manages to capture the "man crab" and to save Daphne. When Velma shows her the newspaper article from Mr. E., Daphne realizes that that two of the kids in the newspaper photo are the same kids as in the picture in the locket she had found in the Crystal Cove caves.

Villain: The Man Crab/Bud Shelton

The children of Crystal Cove are being turned into monsters by a creature named Que Horrifico scaring all of the adults in town. Velma tries to get Shaggy to stop saying the word "like" so frequently as well as to start wearing new pants. Meanwhile, Fred is getting tutored by an intelligent child who claims she should be in college. As the gang try to stop Que Horrifico, they find themselves trapped in a house for sale at the mercy of the "spookified" children, but escape thanks to a children's TV program.

There's a new girl at Crystal Cove High: Alice May, who Fred falls for, much to Daphne's irritation. Alice May is shown to be a ghost with a reputation for taking guys to the prom and making them disappear forever. Shaggy is faced with the dilemma of either going to the prom with Velma or watching a Vincent Van Ghoul movie marathon with Scooby-Doo. As the mystery progresses a connection is made to Deacon Carlswell, the Creeper from the Scooby-Doo, Where Are You! episode "Jeepers, It's The Creeper". There is even a flashback to the old series. The gang also find an old high school yearbook and discover that there was a previous team of teen mystery solvers named "Mystery Incorporated". The episode ends with the appearance of Mr. E.'s mysterious subordinate who reveals his employer's role in the mystery of Alice May. Mr. E. is said to have wanted the gang to "start looking into the real mystery hiding beneath Crystal Cove -- a mystery that led to the disappearance of four youths; a mystery whose time has come to be solved".

Overarching Mystery Clue: An old Crystal Cove High School yearbook

The Hex Girls, Velma's favorite band, come to Crystal Cove to give a concert. But things go awry when an evil specter attacks with the intention of permanently taking The Hex Girls out of the music business. Meanwhile, Scooby-Doo and Shaggy are having a fight because of the latter's prom date with Velma. Scooby even goes as far as getting a new best friend: Harry, a ventriloquist dummy. Daphne is abducted by the Phantom, which makes Fred realize that he has feelings for her. At the same time, Velma shows a few signs of jealousy toward Scooby-Doo.

Villain: The Phantom/Daniel Frezette (Fantzee Pantz)

The gang attends the Royal Knights Fair in Crystal Cove where an evil gnome is paralyzing everyone wearing pirate costumes because it is historically inaccurate. Velma reveals to Daphne and Fred that she and Shaggy have been secretly dating. Shaggy is captured by the gnome, leaving Velma very worried. With some help from Mr. E the gang rescue Shaggy and solve the mystery. The episode ends with a fully cloaked person bumping into Velma and dropping a box. Inside Velma finds a note from Mr. E. encouraging her to pursue her relationship with Shaggy saying, "Don't give up. This has all happened before." The box also contains a picture of the original Mystery Incorporated team with their parrot, Professor Pericles, circled in red.

Overarching Mystery Clues: A photo of the old Mystery Incorporated team highlighting their parrot Professor Pericles. A note from Mr. E.

Two giant monsters, named Humongonauts by Sheriff Stone, are attacking Crystal Cove. Each Humongonaut attacks properties the other brother insures to gain money and revenge against each other for abandoning the other from the circus. Meanwhile, Scooby stumbles across Velma and Shaggy kissing, and discovers their relationship. Shaggy gets into a dilemma when Velma and Scooby fight over who he likes better, and he is forced to decide. Fred decides that the gang should have a name, "Mystery Incorporated", in honor of those that came before them. Unfortunately he also decides that the gang should start wearing team uniforms. Once again Mr. E. intervenes to help the gang solve the mystery.

Villain: The Humongonauts/Max and Jax Minner

Crystal Cove is terrorized by a mysterious violent dog. Sheriff Stone immediately blames Scooby-Doo and arrests him. Meanwhile, the gang is introduced to an old classmate of Velma's, a nerd named Jason Wyatt who still has a crush on her. The gang visits Scooby at Crystal Cove's Animal Asylum "for the Criminally Insane" and encounters Professor Pericles, who gives them a warning, meant specifically for Fred: "Beware of those close to you!". The aged parrot is said to have the "smartest brain in the world" and is shown to apparently possess mystical powers as he convinces a guard that his hand has mysteriously become duct taped to his stun gun. After finding part of a robotic leg at the crime scene, the gang is able to solve the mystery and clear Scooby's name. Shaggy realizes how much Scooby means to him, and decides that he's not ready to have a girlfriend, leaving Velma heartbroken. The episode ends with the news of Professor Pericles' escape from the Animal Asylum. Velma then receives a text message from Mr. E. telling the group to "follow the parrot".

Overarching Mystery Clues: A cryptic warning from Professor Pericles. A text message from Mr. E.

Villain: The Fright Hound/Robot dog controlled by Mrs. Wyatt

A vampire is loose in Crystal Cove stealing what appear to be random items. Things have become strained within Mystery Incorporated, and this time, the gang is truly torn in half. Velma refuses to speak to Shaggy, and Fred and Daphne begin to grow apart. The girls decide to investigate separately from the boys. Daphne and Velma begin to suspect that the vampire may be Daphne’s mother. After receiving help from a mysterious man, Daphne figures out the connection between the stolen items. The gang ultimately unites to capture the vampire, but Velma declares that "maybe we're not a team anymore". The episode ends with the gang returning to their homes separated. Daphne's helper is revealed to be Mr. E.'s mysterious subordinate from "The Legend of Alice May", who observes the gang through binoculars from afar.

Villain: The Vampire/Sheila Altoonian

Following the break-up of Mystery Incorporated, the gang decides to move on with their lives by taking a weekend to check out a nearby university, but they are forced to delay their plans when the campus is terrorized by a mysterious creature known as Char Gar Gothakon, whose screams can destroy anything in its path. With the help of Professor Harlan Ellison and Professor H.P. Hatecraft, they manage to find out why the creature is after Professor Hatecraft. After catching Char Gar Gothakon, the gang reunites only to find that Mr. E has left them a box belonging to the Darrow family, along with a note which reads that the old Mystery Incorporated might never have disappeared if they had this box in their possession. Upon opening the box, its contents are revealed to be an entire history of Crystal Cove. Velma states that it seems that one mystery has now become two.

Overarching Mystery Clue: Darrow Family Archives stolen from the university by Mr. E.

Villain: Char Gar Gothakon/Howard E. Roberts

The gang investigates after Crystal Cove begins suffering from an infestation of deadly insects that targets workers of the company Destroido, the company that makes Shaggy and Scooby's favorite snacks. The cicada monster threatens to destroy Mystery Incorporated on the day of Mayor Jones' Cicada Creature Festival if they don't stop investigating. At the end of the episode, Daphne goes on a date with Fred to the museum's trap exhibit.

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.

Villain: Lord Infernicus/The Funky Phantom

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.

Villains: Shadow Orc/Maxwell the Copyboy

When the entire town of Crystal Cove is taken over by Aphrodite's love spell, Scooby-Doo and the recently escaped Professor Pericles must save the gang and the town from the spell. Working together, they manage to solve the mystery. Ed Machine reveals to them that Professor Pericles had ulterior motives, by showing a recording of Pericles himself, in which he says that giving Scooby what he needed to complete his revenge enabled him to look for certain objects he required. Pericles also has a message for Mr. E, in which he says "The next move is yours, Mr. E".

Overarching Mystery Clue: A warning from an associate of Mr. E.

Villain: Aphrodite/Amanda Smythe

When the gang goes on a quest to find out what happened to the original Mystery Incorporated group on one of their last cases of the 75-year-old disappearance of the Darrow Family and their mansion, they find themselves trapped in the underground Darrow Mansion, which is full of booby-traps. What they do not know is that they are not alone inside the Darrow Mansion, and that someone is trying to kill them, in order to protect something which the original Mystery Incorporated was looking for. In the end, the gang solves the mystery and they collect a strange piece of a planispheric disk, which they believe might be cursed and that is essentially one of the key elements of that mystery, vowing to find out what exactly is the story behind it.

Overarching Mystery Clue: A puzzle piece

Villain: The Phantom in the Radio/Danny Darrow

When exchange student 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 come under attack by the White Wizard who is after Mai Le's ring, but then the Red Wizard comes to the gang's rescue, but is too late to save the ring from the White Wizard. The Red Wizard turns out to be Mr. Chen, the owner of Chen's Internet Café and Tea House. He reveals that, now in possession of all four rings, the White Wizard is able to open the Jade Dragon's Heart, which is a priceless ruby. But, not everything is what it seems in this mystery.

Villain: The White Wizard/Mr. Wang

Scooby and Shaggy win an essay contest to have dinner with Vincent Van Ghoul. When they arrive at the mansion, they are attacked by monsters that seemingly came out of Van Ghoul's movies. Not only that, they are attacked by a monster who calls himself Nightfright, which does not belong to any of the actor's movies, who states that he wants to kill Van Ghoul. This causes Van Ghoul to reveal that he had used the essay contest to start a new TV show and that Nightfright is not part of it. Trying to escape only to find out they are locked in and can't leave until morning, Shaggy calls the gang and they come to help the three, in hopes of finding out why Nightfright is really after Vincent Van Ghoul.

Villain: Nightfright/Arcus Fentonpoof

Velma is feeling lonely without the gang or any friends. Then she receives a message about "Fish Freaks" in the area around an abandoned oil rig owned by Destroido Corp. Velma decides to investigate by herself. She then discovers that a mermaid called Amy was the one who sent her the message. Amy tells Velma that she knows her and that she needs her help, when the Fish Freaks come out of nowhere and try to grab Velma. She manages to escape and then later asks the gang to help her out. They investigate the oil rig, and manage to capture the Fish Freaks. Plus, thanks to Amy, Velma finds out that Angel is not who she says she is.

Villain: Fish Freaks/Ernesto and his group of activists

When Mayor Jones buys an ancient Persian temple on a mysterious website for Crystal Cove's "Creepy Spooky Terror Land," he finds out that there is a manticore who is eating the park's visitors. Having no other option, he asks Fred and the gang to help him capture the manticore. While the gang is investigating, the mayor snoops around Fred's room for the pieces of the planispheric disk.

Villain: Manticore/"Hot Dog Water"

When Fred's favorite adventurer, Dr. Rick Spartan, begins teaching the biology class at Crystal Cove High School, the gang gets to meet him. After Fred and Spartan have a long conversation, Spartan invites the gang to have dinner at his house. At Spartan's house, he shows Fred his latest discovery, a cursed shrunken head. But when its headless body appears and threatens to pursue Spartan until he dies, the gang decides to help Spartan to find a way to break the unending curse. Meanwhile, Shaggy and Velma try to rekindle their relationship, but Velma no longer has the same feelings for Shaggy that she once had.

Fred's dad is being attacked in his home by an unknown shadowy figure, and the gang has to get to the bottom of the mystery. The gang discovers a second piece of the planispheric disk that the mayor is hiding, and finds that Pericles is the one responsible for the attacks on the Mayor. When asked about the mayor's piece of disk, Pericles states that the mayor stole it from him a long time ago.

Overarching Mystery Clues: A warning from Professor Pericles, who also reveals to Mystery Incorporated that the puzzle piece is part of the planispheric disk.

Villain: Shadowy Figure/Professor Pericles

While the gang and Sheriff Stone are chasing the Piranha-Goat, the ghost of Crystal Cove's best sheriff, Dead Justice, comes back from his grave to make Sheriff Bronson Stone quit his job. Dead Justice is trapping Crystal Cove's top criminals, including the monster Piranha-Goat, making Sheriff Stone look bad. The gang eventually captures Dead Justice and solves the mystery. Fred asks his dad if he is proud of him for solving the mystery, but Mayor Jones answers no. Fred and Daphne then go to the Clam Cabin and Fred explains how Daphne is the only one who really understands him. He then asks her to marry him after the end of high school. Daphne agrees, and they share their first kiss together.

Villain: The Ghost of Iron Will Williamson (nicknamed Dead Justice)/Deputy Buckner

The gang is attacked by a hi-tech assassin called the Obliteratrix, who tells them that they all have to die. This leads the gang to investigate the mystery of the Cursed Treasure further with the assistance of Professor H.P. Hatecraft. Along the way, they discover the fate of the original Mystery Incorporated. In the end, Angel Dynamite (Cassidy Williams) traps the Obliteratrix and they solve the mystery. Plus, unknown to the gang, a mysterious creature called "The Freak of Crystal Cove" watches them from the shadows, saying that in the end, the curse will end with them.

Overarching Mystery Clues: Details on the purpose of the disc and the truth behind the fate of the original Mystery Incorporated.

Villain: Obliteratrix/Alice May

The gang goes after the Hidden Treasure of Crystal Cove but are stopped by "The Freak of Crystal Cove". As the mystery progresses, people are revealed for who they truly are and Professor Pericles returns and steals both pieces of the planispheric disk. In the end the mystery is solved; however, the gang tragically falls apart. Fred leaves to go look for his real parents, breaking off his engagement with Daphne, while Shaggy's parents decide to send him off to military school and then send Scooby to a "nice" farm. All seems lost for Mystery Incorporated, but Scooby, enraged at Professor Pericles, vows to bring the gang back together so that they can continue pursuing him.

Overarching Mystery Clues: The circumstances that lead to the original Mystery Incorporated being run out of town and Fred's real parents are revealed to be Brad Chiles and Judy Reeves from the original Mystery Incorporated.