As a boy at school, Ned consoles himself and brings back the memory of his dead mother by slipping into the kitchen at night and baking a pie. Inspired, he decided to become a pie maker.
In the present, Ned is helping Chuck set up her beehives on the roof of the Pie Hole, although she doesn’t want to say why she’s planning to make so much honey. Ned isn’t happy about surprises, having had enough in his life. Later downstairs, Ned and Olive are awkward around each other after their brief recent kiss. They are both unaware that Chuck is still secretly drugging her aunts’ pies with a mood-altering herbal drug. Ned confronts her with his discovery: hidden cupcake tins. Chuck admits that she plans to add to the Pie Hole’s menu by making “cup pies” with honey-filled flour. Ned is less then enthused.
The mother of Anita Grey, a student of the olfactory sciences who is working with renowned odor-memory expert Napoleon LeNez, hires Emerson. LeNez helped her recover the memory of her deceased grandmother by exposing her to the odor of unfiltered cigarettes. She then helped him write his book, “The Smell of Success,” which he plans to publish in the next few weeks. However, Anita was killed in an explosion in LeNez’s laboratory.
At the morgue, Ned revives Anita and she reveals that she was examining a pre-release copy of LeNez’s book and sniffing at the unfiltered cigarette scratch-n-sniff patch to remember her grandmother. The book then blew up in her face. Ned re-kills her and they figure that Anita was the unintentional victim and LeNez was the real target. They go to see the olfactory expert, who lives in a sterile apartment and has them come in through a decontamination chamber. LeNez sniffs each of them and identifies Emerson’s and Ned’s professions. He’s puzzled by Chuck, detecting a faint odor of death on her. She hastily explains that it’s her perfume and they tell the mournful LeNez that Anita wasn’t the intended target. LeNez reveals that his book release has been pushed up on the schedule.
Chuck visits Lily and Vivian and goes through their old mermaid costumes, trying to rekindle their interest in synchronized swimming. Even Lily starts to cheer up until they find Chuck’s old sweater. Lily becomes more depressed then ever and tells Olive to haul it all away.
While Chuck tries to sell Ned on her cup pie idea, Emerson figures they should look at the book that was bumped for LeNez’s release. The trail leads to Chas Spielman, who is releasing a pop-up book for adults. Chas says that LeNez’s book is actually being bumped out of the prime holiday spot and denies having anything to do with the murder.
Inspired by LeNez’s book, Chuck gives Olive chlorine tables to try and reawake her aunts’ memories. They find a stinking stock jammed in the Pie Hole’s sink, with a warning for them to give up the LeNez case. They show the warning “note” to LeNez, who confirms it came from the sewer and can only have come from one man: Oscar Vibenius. Oscar and Napoleon were partners until they disagreed violently over their respective theories. LeNez believes in the purity of odor while Oscar favored natural scents. Oscar retreated into the sewers and LeNez believes he’s making sure that “The Smell of Success” never sees publication.
Olive visits Lily and Vivian and tries to get them interested using the chlorine tablets. Vivian responds but Lily resists the memories. Meanwhile, the trio of investigators go into the sewer and fine a large yellow hose. They follow it to a methane juncture pipe where they find Oscar working on the valve. They all panic and run off. The hose runs up into the sewer and into LeNez’s car. He arrives and activates his remote, setting off a huge explosion.
The newest murder attempt makes the news and Oscar is accused of murder. LeNez is meeting with the press and Emerson and Ned are going there as eyewitnesses. Chuck goes to see Olive at her apartment, and Olive is trying on the aunts’ mermaid costume. She shows Chuck her old sweater and Chuck starts crying, and insists that the aunts need to move beyond their grief.
LeNez and Emerson talk to the reporter on the television, while Olive and Chuck watch them at the Pie Hole. Oscar comes in and asks for pie and conversation. Olive holds him at knifepoint and they reluctantly hear him out. First he notices Chuck’s odor and is intrigued, but unlike LeNez isn’t put off by her claim that it’s perfume. He notes that neither of the murders were successful and he must not be a very good murderer, then explains that he was trying to find out who the murderer was and followed the yellow hose through the sewers. He was trying to unattach the hose when Ned and the others found him, and when they interrupted he didn’t have enough time to save LeNez so he had to run for cover. They go to the site of the explosion and they all recognize the scent of rotten eggs. However, methane doesn’t have an odor and they figure only a snob would scent the methane to convince the general public it was a real methane explosion. Finally, they figure that with the two death threats, LeNez’s book sales will skyrocket.
Vivian and Lily are looking at old slides of Charlotte and Vivian forces Lily to admit that didn’t quit because of her eye injury, but because of their grief over Chuck. Lily smells the chlorine tablets again, and starts to smile. Meanwhile, Ned searches LeNez’s apartment during the press conference and shows Emerson what he’s found: another stinking sock with a warning message. They confront LeNez with it but he denies everything and orders them out. However, as they leave he seals them in the decontamination chamber and starts pumping explosive gas in.
LeNez admits that he planted the explosive chemical in the scratch-n-sniff book, but Anita wasn’t supposed to smell it. It was intended to go off and look like a murder attempt, but Anita sniffed it prematurely and died. LeNez then set up the second death threat to make it look like Oscar was responsible for both attempts. Chuck, Olive, and Oscar arrive and enter the decontamination chamber from the other side. However, Oscar has used his knowledge of the city systems to reprogram the decontamination and ventilation systems, and he purges the outside odors of the world directly into LeNez’s apartment. The olfactory expert collapses from the strain and Oscar releases them from the decontamination chamber.
Vivian goes outside and, inspired by the rain and the dawn, starts to sing. Lily smiles some more and the two of them go to the pool and synchronize swim once more.
Ned comes into the Pie Hole and shows Chuck the new menus… with her cup pies. LeNez is taken to jail and Emerson is happy with his new interest: pop-up books. Outside the Pie Hole, Oscar lurks, smelling Chuck’s sweater and trying to identify the unfamiliar odor.
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