In boys’ school, Young Ned ends up as lab partner with fellow outcast Eugene Mulchandani. When Eugene builds a small flying machine out of paper and his classmates almost destroy it, Ned comes to his aid and the two becomes friend. However, when Ned inadvertently resurrects a pile of dead leaves, Eugene runs off in terror, and Ned realizes how ephemeral happiness is.
In the present, Ned finally asks Chuck if he’s her boyfriend and she says yes. Olive overhears it and becomes depressed, ignoring the romantic overtures of Alfredo Aldarisio. Ned realizes it’s the birthday of Chuck’s father, if Ned hadn’t accidentally killed him by bringing his mother back to life.
Emerson announces they have an easy case: Tina hires him to investigate the murder of her boyfriend Tony, who was found strangled by a woman. However, Ned is more concerned with Chuck finding out about his role in her father’s death. They also find out that a new candy store, Balsam’s Bittersweets, has opened up across the street.
Ned brings Tony back to life and he reveals that he was killed by Burly Bruce Carter, who strangled him using a life-size female doll. Apparently Bruce was in love with the doll and when Tony pointed out she wasn’t real, Bruce used the doll’s hands to strangle Tony. Emerson, Ned, and Chuck confront Tony who eventually breaks down and confesses he killed Tony, so that he can protect his “girlfriend” Sheila.
At the Pie Hole, Olive poses a hypothetical to Alfredo about what someone should do if their romantic interest isn’t returned. He says that he’d love them no matter what and no matter if his interest was returned, but Olive doesn’t get the hint. Depressed, Olive goes over to Bittersweets where she’s greeted by siblings Billy and Dilly Balsam. Ned and Chuck bring over a pie but when the customers smell it and go to the Pie Hole, sister Dilly considers it a challenge and declares war on them.
Later, Ned finds Dilly’s first act: she’s sabotaged the “le” in the “Pie Hole” sign. Ned refuses to do anything about it, much to Chuck’s surprise. A health inspector, Andrew Brown, then stages a surprise inspection and finds Ned’s locked storage room filled with the dead fruit that he brings back to life for his pies (and to save costs). Brown closes the Pie Hole but Ned still refuses to take action against Dilly, who tipped the inspector off. Dilly visits them and Ned offers her pie, but when Chuck and Olive turn hostile she admits she’s at war with them and if Ned doesn’t fight back, she’ll win for sure. It’s revealed that Dilly’s parents died of bird flu at Bodega Bay so she traveled there to confront the birds responsible. They attacked her but she was saved by a candy merchant and gained a life-long appreciation of sweets.
Chuck and Olive sneak over to Bittersweet after dark and drop off some rats. One of the rats falls into a taffy vat after they leave, revealing that Billy’s corpse is inside. When Ned finds out what Chuck has done, he goes over to clean up the mess, but inadvertently brings Billy back to life. Billy’s life is filled with taffy so he can’t say anything, and Ned is forced to re-kill him before the minute runs out. The police and Dilly arrive and find Ned standing over Billy’s corpse, and take him away for murder.
Emerson and Chuck go to see Ned and reassure him, then go to the morgue to check on the body. Without Ned, Emerson will have to investigate the normal way, so he goes to check up on Billy’s background while Chuck eagerly watches as the coroner does the autopsy. Olive also visits Ned with a gun in a pie, but he tells her to take it away.
Late, Chuck and Emerson compare notes and determine the autopsy showed that Billy bit off his killer’s finger. However, his gastric acids have destroyed the fingerprints. Ned goes to prison, only to discover that Bruce is his cellmate. Bruce prepares to attack the man responsible for his imprisonment, but Ned distracts him by asking how he met Sheila. Bruce explains that he bought a life-size doll so he could use the carpool lane, but she soon took on a life of her own and they fell in love.
Emerson and Chuck have Olive distract Dilly while they sneak into Bittersweets looking for clues to the nine-fingered killer. Dilly spots them, locks Olive in her trunk, and goes inside to hold them at gunpoint. She’s wearing mittens against the cold but when she removes them to hold the gun, they realize she has all ten fingers. Emerson convinces her that all they want to do is find her brother’s killer and she lets them go.
Fortunately, the finger in Billy’s stomach provides Ned with an alibi, since it had to be in there well before Ned arrived at the store. Further investigation determines that Andrew Brown was the killer. Billy bribed him to do the surprise inspection at the Pie Hole, but Brown blackmailed him for more money. In the subsequent struggle, Billy was killed after biting off Andrew’s finger.
Andrew is wanted for questioning but can’t be found. Ned is released from prison and gets a hug from Olive, and considers it a hug from Chuck as well. Emerson reluctantly admits that while he can do a normal investigation, he’d rather have Ned as a partner. And Chuck and Olive give Ned a welcome home pie.
Later, Olive sees Alfredo’s cup of coffee and imagines him coming in to sweep her off her feet. But he doesn’t come in, and she’s left to think they’ll get together someday.
In his cell, Bruce looks up to the sky and thinks of Sheila, taken away by the authorities but sure they’ll be reunited someday.
In a dismal swamp, Dilly disposes of Andrew Brown. Andrew won’t be reunited with anyone on any day.
Ned and Chuck sleep in separate beds and he considers how much he missed her… and then confesses he killed her father.
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