His publisher demands a darker, grittier Jenny LeClue book or else the series will be canceled, so Finklestein reluctantly responds by giving Jenny her biggest case yet: the murder of the beloved dean of local Gumboldt College, with her forensic science professor mother as the prime suspect.

One day, after solving a few trivial mysteries that includes the likes of figuring out what Dean Strausberry had for breakfast, Jenny complains to Keith about how boring Arthurton is, describing it as stuck in the past.

Jenny tries to leave the crime scene though the window to avoid detection, but a hard landing knocks her unconscious.

Having previously written off Susie as stereotypical blonde bimbo, Jenny is shocked to discover that Susie is in fact a prodigy in multiple scientific fields, but keeps this fact a secret from her own family due to familial pressure of keeping up the appearance of a "Glatz Girl".

Back at her home, now surrounded by police, Jenny sneaks into the basement to look for a spare change of clothes and detective gear.

She is shocked to discover that a mysterious man in a trench coat, face completely obscured, is also inside her home looking for something.

Piecing together a shredded note discarded by the man, Jenny realizes that there is a secret entrance to the abandoned underground mines in the graveyard, which will connect to the sewer system and ultimately, the prison.

She asks Susie and Keith to distract the police while Jenny races back to the grave site of where the Dean was buried.

Throughout her excursion, Jenny had been uncovering evidence of a massive secret research project in Arthurton, one that caused the alleged death of her dad.

The Dean chose to disappear from the public eye in order to help Jenny's mom take down the shadowy organization responsible for sponsoring this secret project, which they had deemed an existential threat to their town.