Daphne wasn't able to fit into the "bridal air-lock", at the wedding of one of her sisters, because she had swollen up so much from eating shellfish.Daphne and the gang solved the mystery of the Creeper when she, the Creeper and the rest of the gang, except Scooby-Doo, were trapped in hay-sacks and Scooby unmasked the Creeper who was actually Deacon Carlswell.
We first see Daphne being sent to jail with the gang after solving another mystery but when a slime mutant has been rumoured to live underneath Crystal Cove is cocooning anyone who gets in its way the gang looked into solving the mystery, Despite being warned not to continue investigating by her parents, Daphne attempts to solve the mystery along with the gang.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".Crystal Cove is being terrorized by a mysterious Ghost Truck that has been running people off the highways. 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 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.
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.
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. Daphne is abducted by the Phantom, which makes Fred realize that he has feelings for her.
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.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. 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. 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.
Daphne goes on a date with Fred to the museum's trap exhibit.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 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. However the Blake Family are left less than impressed when Fred attempts to stop the wizard by setting off traps, this gives a worst impression of Fred to the Blakes.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
Following the disbandment of Mystery Incorporated, Mayor Janet Nettles, Mayor Fred Jones Sr.'s successor, is approached by a mysterious figure, who later turns out to be Velma. She shows the mayor files on her fellow mystery-solvers in order to seek their help in bringing down Crybaby Clown who is torturing Crystal Cove.However after the knowledge that Daphne is coming back, Fred is depressed that the villian escaped and states that Mystery Incorporated won't be the same since Daphne is never coming back.
The gang are looking to replace Daphne and Velma suggests Hot Dog Water, who is out on parole for helping making the jail more cruel.
Fred tries to get Daphne back while Crybaby Clown returns to rob Crystal Cove, kidnapping a therapist, a hairdresser, a plastic surgeon, a publicist, and Daphne as well. The gang chase Crybaby Clown to an airport where he is about to take off with the five captives but is stopped by Mystery Incorporated and they solve the mystery. Daphne agrees to return to the gang. With Daphne back on the team, Hot Dog Water is removed as a member.