After accidentally destroying Folsom's birthday party, Fillmore and Ingrid are asked to do convention duty. However, the train convention experiences sabotage, leaving the entire convention ruined. Fillmore and Ingrid first suspect the RC Car Club to be behind it, but the evidence points in the other direction.

Fillmore's partner moves away to Tennessee, and he is partnered up with Brad Parnassus, the smartest kid at X Middle School. Rebellious and super-smart new student Ingrid Third doesn't take her introduction to X student body well at all, and a giant stink bomb soon explodes in the hallways.

Scooter thefts are up, and the Safety Patrol faces a challenge from student activist Derek Minna, who establishes B.A.G.A.S.T. (Boys And Girls Against Scooter Theft), a scooter and rollerblade equipped task force that he intends to ultimately replace the safety patrol. Fillmore and Ingrid trace the thefts to the Metal Shop and infiltrate the gang in an attempt to take down the culprits.

Vallejo's nearing his second term test for Junior Commissioner, and in the meantime, a crime crops up involving "The Shredder", an anonymous criminal who shreds people's pet projects. Unfortunately, not a single one of the victims saw the Shredder's face. This seems like a job for Vallejo's old profiler partner, Frank Bishop, who was driven from the Safety Patrol in disgrace. He is tasked to deduce a pattern to the Shredder's crimes and discover who is next on the list.

Fillmore and Ingrid investigate the mysterious vanishing of a student named Alexis, only to find that all reports of her have vanished from the school, and she's even been taken out of pictures. Meanwhile, someone is working on a computer virus called Electric Haircut, which must be stopped before it causes any irreparable damage.

Facing expulsion under Principal Folsom's new "Three Strikes, You're Out" rule, Fillmore must protect the only person capable of clearing his name to a crime he has been framed for—the destruction of a giant Folsom statue made out of 12,000 pieces of macaroni.