Young Ned and the other boys are in Mr. Galts science class, who lets them choose their own lab partners. Ned ends up with the last one, Eugene Mulchandani, an exchange student from Gorakhpur, India. They end up as friends but when Ned jumps into a pile of dead leaves and brings them back to life, Eugene runs in fear.
At the Pie Hole, Ned asks Chuck if hes her boyfriend, and she says he is. She then says its her fathers 60th birthday if he had lived. Meanwhile, Olive, having overheard, is unhappy and starts spinning on her chair. The only customer they have is Alfredo, who Olive doesnt remember letting in or serving.
Emerson comes in with an easy case but Ned is more worried about how hes responsible for the death of Chucks father. They get word that a new candy store has opened, thanks to a suspiciously enthusiastic stranger. Back to the case: Tina Arongino hires Emerson to clear her of the murder of her boyfriend, Tony DiNapoli. They talk to Tony who says that Burly Bruce Carter killed him and used his girlfriend, a plastic doll, to strangle him. Bruce invited Tony to a double date with his plastic doll but when Tony got there first and pointed out Bruces girlfriend wasnt real, Bruce strangled him with the dolls hands.
Olive talks to Alfredo about her relationship with Ned and moving on, but he says he would stay no matter what if he was in love with someone. Meanwhile, Ned and the others go to see Bruce, who claims Tina killed Tony. He refuses to let them talk to his girlfriend Sheila and he breaks down crying. Bruce is arrested and Tina is freed.
Olive goes to the new candy store, Bittersweets. The stranger who came into the store is there and introduces himself as Billy Balsam, the co-owner. Ned and Chuck bring a pie and Billy introduces them to his sister and partner, Dilly Balsam. When her customers take an interest in the pie, Dilly stutters and declares war. She kicks them out and then reveals she faked the stutter to distract them.
Later Ned discovers that the store sign is damaged to say The Pie Ho, but Ned refuses to accept the Balsam siblings are responsible. Olive offers to let Chuck talk to her about Neds distant attitude but Chuck declines. A health inspector, Andrew Brown, conducts a surprise inspection, and demands to see Neds locked refrigerator. Ned is forced to reveal that its full of dead fruit and Brown closes them down. Olive vows revenge but Ned still doesnt want to take action. Dilly comes to visit and say that its only going to get worse. Ned refuses to fight and she warns that hell lose. It turns out Dilly and Billys parents died of bird flu. Dilly was almost killed by birds while facing her fear of them, but was rescued by a taffy maker so she embraced a life of sweets.
When Ned refuses to take action, Olive and Chuck sneak over to Bittersweets and release rats into the store. They leave, unaware that Billys body is floating in the taffy vat. Ned is still upset but doesnt admit to Chuck hes upset about her fathers death. Ned goes to clean up the rats and reaches into the taffy vat. He touches Billy and brings him back to life. Neds not sure when he touched Billy so he quickly touches him again, but Dilly and the police arrive and arrest him for murder.
Emerson and a disguised Chuck go to see Ned in jail then go to check on the body. Chuck and the coroner examine the body while Emerson checks Billys background. Olive visits Ned and bursts into tears, then brings him a pie with a gun in it. Ned tells her to put it away and Olive cries some more.
Chuck meets Emerson at the Pie Hole and reveals that Billy bit off his killers finger, but his stomach acid erased the fingerprints. In his cell, Ned discovers his cellmate is Bruce, but quickly distracts him by asking him how he met Sheila the doll. Bruce explains how he bought a doll to get into the carpool lane and then fell in love with her. Ned tries to console Bruce, assuring him that hell be back together with Sheila eventually.
Chuck and Emerson sneak into Bittersweets while Olive distracts Dilly, and Chuck finds hand prints from Billys struggle. Emerson lifts the nine-fingered hand print while Olive talks to Dilly who is wearing mittens. Dilly spots Emerson inside and shoves Olive in the trunk of her car. She then draws a gun and confronts Emerson and Chuck, and is forced to remove her mittens to pull trigger, which reveals she has 10 fingers. She finally agrees to let them go so they can find the real killer.
Emerson checks the tests and determines that Billy must have died several hours earlier then when Ned was found. It turns out that Andrew Brown was blackmailing Billy and Dilly after letting himself be bribed to conduct the surprise inspection. Billy was killed in the struggle. The authorities launch a search for Andrew while Ned returns to the Pie Hole and Olive hugs him, while Chuck doesnt. Emerson admits hed rather have Ned helping him. Neds had time to think and realizes that Chuck is happier not knowing Ned is responsible for her father's death. Chuck and Olive bring out a welcome home pie for Ned, who then goes to bed. Olive briefly imagines Alfredo coming in and embracing her. Bruce looks out of his cell and thinks of Sheila. And Dilly disposes of Andrew Browns corpse.
Ned talks to Chuck about her being his phantom limb and then confesses to killing her father.