At the Longburrow School for Boys, Ned dreamed of his mother coming back but once he realized she wasnt, he came up with a way to bring back at least some small part of her. He snuck out to the kitchen and made his first pie, and comforted by the scent, went on to become the Pie Maker.
Ned is helping Chuck set up her beehives on the roof and while she dreams of expanding, hes content to keep it on the one rooftop. He wonders why Chuck needs so much honey and she says she has a surprise for him. Ned isnt thrilled about surprises. Olive and Ned are nervous around each other, while Chuck continues to secretly drug her aunts pies with homeopathic mood enhancers. Ned discovers Chucks surprise: cupcake pans, so she can make cup-pies. Ned prefers to stick with traditional pies.
Emerson receives a call from the mother of Anita Gray, who was a student of olfactory science expert Napoleon LeNez. LeNez was working on using smells to unleash memories, and helped her to remember her grandmother. Together they created a self-help guide, The Smell of Success, but Anita was killed by a mysterious explosion.
Chuck, Emerson, and Ned go to the morgue to revive Anitas corpse, and she reveals that she was sniffing a scratch-'n-sniff patch of unfiltered cigarettes in the new book (to remember her grandmother again) when the book exploded. Emmerson suspects that someone was trying to kill LeNez.
The trio goes to see LeNez, who puts them through a decontamination chamber. He then examines their scents and notices an odor of death about Chuck, believing its from her perfume. Chuck hastily covers by agreeing. They explain that the scratch-n-sniff patch was designed to explode. LeNez is unhappy about Anitas death and reveals that the books release was pushed up on the release schedule.
Olive goes to Lily and Vivian to collect items for them to sell, and admire their mermaid gear. Admitting shes a fan of the Darling Mermaid Darlings, she tries to get them interested in reviving their career but finds a sweater belonging to Charlotte. Lily is more depressed then ever and tells her to take everything away.
Emerson suggests that they see whose book got bumped when LeNezs got pushed forward, while Chuck pursues her cup-pie idea. Olive pulls Chuck away to explain about Lily and Vivian and Chuck wants Olive to push harder. Ned is concerned about the two women bonding. Emerson realizes that the bumped book was a pop-up book entitled "Pop-Up Pin Ups". Ned and Emerson go to Pop-Up Palace to see the pop-up book author, Chas Spielman. Spielman denies attempting to kill LeNez and notes that the publisher moved LeNezs book from a holiday spot to a dead sales period.
Chucks newest scheme to cheer up her aunts is to expose them to the smell of chlorine and revive their memories of their synchronized swimming days. The trio returns to the Pie Hole and finds a drain clogged with a stinky sock with a warning written on it: "u can't save lenez". They take the sock to LeNez who says it could have only come from one man, Oscar Vibenius. The two of them were lab partners until they split up over their odor theories: Oscar believed in more natural odors. Afterwards Oscar retreated below ground to the sewers. LeNez believes Oscar is trying to stop the publication of his book.
Olive visits the aunts and exposes them to the smell of chlorine. Lily seemingly starts to smile but then belches and returns to her despondency. Ned, Emerson, and Chuck go into the sewers to look for Oscar and follow a yellow thick hose to LeNezs apartment building, where they find Oscar working on a methane gas outlet with a hose leading up to the surface and LeNezs car. The trio run in terror from Oscar, while above LeNez activates his remote car lock and the vehicle explodes.
The explosion makes the news and Oscar is wanted for the attempted murder of LeNez. Chuck is cleaning up at Neds apartment and they note that Oscar isnt very good at his murder attempts. Emerson is meeting with LeNez to give a press statement. Chuck goes to see Olive, who is trying on the aunts mermaid costume and gives Chuck back her sweater. Chuck starts to cry, much to Olives dismay.
LeNez and Emerson are interviewed by a reporter about the attempts on LeNez's life. LeNez says that someone doesnt want his book published and implicates Oscar. Chuck and Olive watch the broadcast at the Pie Hole as Emerson gives a brief advertisement for himself, but then Oscar comes into the diner. Olive goes for a knife but Oscar says hes just there for pie and talk, and notes he doesnt appear to be a very good killer. They agree to hear him out, and Oscar explains that while investigating the case from the sewer, he spotted the hose and tried to shut it down. The trio found him before he could shut it off, and he had to run for cover before the explosion. Oscar smells Chuck and notices something unusual, and doesnt believe her claim that her perfume smells of death. They realize that the methane explosion smelled like rotten eggs, but methane doesnt have a smell. Only someone who believed the public was dumb enough to think that methane smelled of rotten eggs would have rigged the gas to smell that way. Oscar notes that LeNezs book sales are guaranteed to rise after the publicity from the murder attempts.
Lily and Vivian are going over old slides of Charlotte, and Vivian notes that they didnt quit because of Lilys eye injury, but because of their unhappiness. Lily smells the chlorine tablets again and starts to remember.
Meanwhile, Ned searches LeNezs apartment during the interview and reveals what hes found to Emerson. Emerson and Ned confront LeNez with the evidence: another smelly sock with a warning message. They accuse him of framing Oscar, but he accuses them of planting evidence. He orders them out but traps them in his decontamination chamber. He then pumps in explosive gasses that will explode when sets it off. LeNez reveals that Anitas death was an accident. He rigged the book to explode but didnt expect her to secretly sniff it. He then staged the second murder attempt and framed Oscar.
Chuck, Olive, and Oscar arrive and enter the decontamination chamber, and reveal that Oscar reprogrammed the decontamination system. He reverses the airflow, pumping all the odors of the outside world into LeNezs apartment. LeNez collapses, overwhelmed by all the natural scents.
At the aunts home, Vivian bursts into song and she and an inspired Lily go to the pool to synchronize swim. Emerson closes the case and enjoys his newly-regained interested in pop-up books. Ned shows Chuck his new menu with cup-pies. Outside, Oscar lurks in a van and watches Chuck, obsessed with trying to identify her unique odor and smelling her stolen sweater.