Season 2 Episode 1
Crystal Cove is attacked by a Man-Baby called Crybaby Clown. Mayor Fred Jones Sr.'s successor Janet Nettles is approached by a mysterious figure who gives her the files on Mystery Inc. while stating that she has to get Mystery Inc. back together. She starts by picking up Scooby-Doo from a farm, introducing herself to him and telling him of her mission. At a military school, Shaggy is being scolded by his drill sergeant for not shaving the hairs on his chin until Scooby crashes into the barracks in a tank and gets Shaggy out of there. Fred (now resembling a hobo) is still looking for Brad Chiles and Judy Reeves and is convinced by Shaggy and Scooby to give up his search for them for now. Upon driving back to Crystal Cove, Fred tells Shaggy and Scooby what he knows about a Man-Clown. Upon finding Crystal Cove deserted, the three are attacked by Crybaby Clown. Fred is then chased by Crybaby Clown until he is saved by the mysterious figure who turns out to be Velma, as Shaggy and Scooby catch up. Upon being briefed by Velma on the Crybaby Clown attacks sometime after Mayor Fred Jones Sr. was arrested, Scooby tells Shaggy, Fred, and Velma that Professor Pericles survived. Velma later shows Fred from outside the Bloody Stake restaurant that Daphne is seeing a guy named Baylor Hotner. Mayor Nettles and Sheriff Bronson Stone bring Shaggy, Scooby, Fred, and Velma into City Hall where the rest of the citizens are waiting for Mystery Inc. to come and stop Crybaby Clown. Colton and Paula are surprised that Shaggy and Scooby are out of the military school and farm. Just then, Crybaby Clown crashes the assembly and traps everyone inside. After the group escapes from City Hall, they go to Daphne's house and try to get her to rejoin with no avail. 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, planning to use one of his bottle bombs to blow up Chen's Fireworks. Fred is depressed that the bad guy got away and states that Mystery Inc. won't be whole again since Daphne is never coming back.