Following the disbandment of Mystery Incorporated, Mayor Fred Jones Sr.'s successor Mayor Janet Nettles 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 terrorizing Crystal Cove. Mayor Nettles sets out immediately to retrieve Scooby-Doo and break him out of the pound he is in. Scooby then helps Shaggy escape from military school and together they find Fred (who now has the appearance of an old hobo) and the three return to Crystal Cove. Velma joins them and together they go to bring Daphne back, but she refuses their offer, as she has a new boyfriend now. Fred comes up with a doughnut shop-themed trap in order to trap out Crybaby Clown. The trap doesn't work and Crybaby Clown escapes using one of his bottle bombs to blow up Chen's Fireworks. Fred is depressed that the villain escaped and states that Mystery Incorporated won't be the same since Daphne is never coming back.