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Season 1EditWe first see Velma 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, Velma attempts to solve the mystery along with the gang. However Velma has been trying to get Shaggy to be more intimate in their secret relationship. However 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".
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 in Gatorsburg however she was grabbed by the green gator person, but Shaggy saved her and the Creeping Creatures were sent to jail. When Scooby got scared by lightning and jumped on Shaggy, he held Velma's hand.The gang receives an old newspaper article from Mr. E about four kids who disappeared in the Crystal Cove caves many years prior. Velma shows the newspaper article from Mr. E. to the gang, 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.
As Velma and Shaggy's relationship grows, Velma realises the more and more faults of Shaggy so attempts to fix them, Velma tries to get Shaggy to stop saying the word "like" so frequently as well as to start wearing new pants.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.
The Hex Girls, Velma's favorite band, come to Crystal Cove to give a concert. Meanwhile, Velma and Shaggy's relationship is getting worst, 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.Velma shows a few signs of jealousy toward Scooby-Doo.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.
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.The gang is introduced to an old classmate of Velma's, a nerd named Jason Wyatt who still has a crush on her. Shaggy realizes how much Scooby means to him, and decides that he's not ready to have a girlfriend, leaving Velma heartbroken.
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.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.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. Shaggy and Velma try to rekindle their relationship, but Velma no longer has the same feelings for Shaggy that she once had.
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.
Velma and Hot Dog Water are discovered to be working for Mr E. and are going on missions for him; here they go to Russia to retrieve a piece of the Planaspheric Disc from an old house, but when they are stopped by the nightmare witch Baba Yaga they buy it and bring it to Crystal Cove where the house springs chicken legs and rampages over town. Meanwhile, 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.