Ned discovers he has the ability to raise the dead for one minute by touching them. If he touches them again they die. If he doesn’t touch them within one minute, someone else in the vicinity dies. As a young boy, Ned first revives his dog Digby, then revives his mother when she dies but when she lives more than a minute, next-door neighbor girl Chuck's father dies. Ned later touches his mother again and she dies for good. Ned and Chuck briefly kiss during their parents' mutual funeral, and then Ned's father takes him to boarding school while Chuck's aunts Lillian and Vivian raise her as their daughter and teach her beekeeping.
As adults, Ned makes pies for a living to remember his mother the cook. Chuck is murdered on a cruise. Ned, visiting, brings her back to life and, loving her, refuses to touch her again. Now the two can never touch or Chuck will die for good.
Ned is help Chuck with the bee colony she keeps on the roof of their apartment over the Pie Hole, and that died due a pesticide accident. He has to strip to his underwear and as a courtesy she does the same. She then puts on protective bee-harvesting clothing. They chat and Ned admits that he hasn't seen his father in years. Chuck then reveals why she had Ned strip: she pours the bees all over Ned and they're brought back to life, while all the other insects in the area die.
Emerson Cod is working on his new pop-up book, "Lil' Gum Shoe," when Dusty Fitts comes in and wants to hire Emerson to solve the murder of her wife Kentucky. She supposedly died in a work-related "accident" with bees but Dusty doesn't believe it. Further, he had overheard his wife talking about having an affair with someone and leaving "him." Dusty doesn't know if she meant she was going to leave him, or her secret lover.
As it turns out, Kentucky Fitts worked for Betty's Bees, a company that uses the honey from bees in all of its freshly made products. Kentucky was the company's Number 1 Bee Girl, and was found dead at the wheel of her car, stung to death. Emerson takes Ned and Chuck to the morgue and Ned brings the boil-covered Kentucky back to life. She says she wasn't having an affair and was going to leave the company. She kept the news secret from Dusty because she didn't want him knowing she as sabotaging the company's bees with a "lot of might." All Kentucky can say about her murderer is that she didn't see his face, but he or she spit something at Kentucky and then the bees stung her to death. With the minute running out, Ned makes Kentucky dead again. He hears a humming sound and backs away as a swarm of bees emerge from Kentucky's mouth.
At the Pie Hole, Emerson wants to use Chuck as an undercover operative at Betty's Bee, since they're looking for someone to replace Kentucky. Ned objects because of the danger but Chuck agrees to go. She interviews with Woolsey Nicholls, the new owner of Betty's Bees. Woolsey also owns Bzzzzzzz!, a rival honey-based product company, and recently bought out Betty's Bees. He kept on Betty but felt she was too old and wants Chuck as the new Bee Girl. As Emerson and Ned listen in on Chuck's bee lapel with a hidden bug, Woolsey hires Chuck. Chuck then sneaks into Kentucky's old office and finds a key in her desk. However, she also finds Betty Bee in a closet. Betty claims she is treating herself for claustrophobia using aversion therapy then demands to know who Chuck is. Betty then storms out, taking the key with her.
As the trio goes over at the case at the Pie Hole, Olive wonders if an inter-office romance is involved. The others figure it isn't, but it's clear Olive has a different inter-office romance in mind. Olive's also concerned about the fact that she knows who Chuck's real mother is: Lillian, who admitted it while under the effects of a drugged pie. Olive can't tell Chuck Lillian's secret, and can't tell Lillian that Chuck is alive. They're interrupted when Lillian and Vivian come to visit the Pie Hole. Vivian wants to know why Olive hasn't been visiting: Lillian ordered Olive away after the latter learned her secret, and tried to keep Vivian away without success. Chuck quickly hides behind Emerson and Olive snaps, screaming at the top of her lungs. Ned insists she can't go but Olive doesn't want to hear about it. Lillian says she knows a place where Olive can stay.
Ned and Chuck go to check out Olive's apartment and water her plants after she leaves. Chuck looks around the place appraisingly and admits that she'd been drugging her aunts so they'd get out of the house after years of isolation. Ned realizes that Chuck is going to move out of his apartment and into Olive's apartment. Chuck thinks it will be romantic but Ned disagrees.
Olive is happily singing and dancing… until the nuns at the nunnery where she's now living tell her to shush.
Back at Betty's Bees, Woolsey introduces Chuck to Betty. Betty explains that Woolsey took over the company in a hostile takeover and demoted her. When Woolsey took over, the company's bee colony died under mysterious circumstances, infected with mites. However, Betty insists it was an accident and Woolsey couldn't have been responsible. Betty waxes poetic about her childhood and the home that she nicknamed the "Honey House," and how she's been raising bees since she was five.
Chuck meets with the others at the Pie Hole and they talk to Dusty, explaining what they've learned to date. Dusty notes that Betty and Kentucky were like sisters and finds it hard to believe anything could have come between them. However, at least now he knows that Kentucky wasn't having an affair. Chuck plans to get the key the next day and is puzzled that Ned doesn't raise any objections. Chuck is forced to hide when Vivian shows up. Ned goes outside to talk to her and Vivian talks about how she misses Chuck, and they've kept all of Chuck's belongings in her childhood room. Lillian has disappeared, and Vivian has no idea where she is. Interested, Ned listens as Vivian talks about all of Chuck's belongings.
The Mother Superior at the nunnery informs Olive that she'll have to give her belongings to the poor. Olive is less than thrilled. When she starts complaining, the Mother Superior tells her she'll have to live like a nun if she's going to stay there and give birth. Olive quickly corrects the Mother Superior's mistaken idea, then realizes that Lillian lived at the nunnery while she was pregnant with Chuck.
Chuck arrives at Betty's Bees to find Ned working there as a temp for Betty: he "pruned" her assistant's pie then intercepted the call for a replacement and got himself hired as a temp. Chuck is flattered and then sneaks into Betty's office when Betty calls Ned to go with her on her rounds. Chuck finds the key and a photo of a five-year-old Betty with a bee beard standing in front of a house. Turning, Chuck finds herself-face-to-face with a figure covered in bees.
Ned and Emerson come after Chuck and find her covered in bees, sitting perfectly still. Ned uses a hat stand to push her to the window where she spits out a container holding a queen bee. The bees fly off after their queen and Chuck explains that the murderer spit the container into her mouth, and the bees covered her over. Unlike Kentucky, she remained calm and the bees didn't sting her to death. They see the photo of Betty with her bee beard and wonder if she's killer. The house number matches the number on the key and they conclude that it's Betty's childhood home, the Honey House.
Olive goes into the nunnery's confessional to file a police report on her stolen goods, only to find Lillian waiting for her. Lillian suspected that Olive might try to leave, but then has to admit that she has a further secret: Chuck's father was Vivian's fiancé. Lillian wants to make sure Olive never tells Vivian any of this. She suggests that olive should stay in the nunnery because she's having man troubles and a place with no men is the best place to sort them out. Olive reluctantly agrees but begins to wonder exactly how long Lillian wants her to stay there.
Ned, Chuck, and Emerson put on protective clothing and go to the Honey House. It's covered with bees: the supposedly dead bee colony wiped out by mites. Betty confronts them, but they've figured most of it out. Betty and Kentucky worked together to fake the bee colon's death to sabotage Woolsey's purchase, then hid the bees at the Honey House. Betty says that Woolsey killed Kentucky but can't reveal her knowledge without incriminating herself for industrial sabotage.
Everyone goes to Woolsey's office and Emerson reveals they have the evidence they need: the queen bee container, with Woolsey's spit on it. He was the one who covered himself in bees and spit the container into Kentucky's mouth. The police take Woolsey away.
Betty takes Dusty on a partner and they open up the Honey House as a new company.
Ned brings all of Chuck's belongings from home and sets them p in her apartment, accepting her decision.
Emerson finishes the "Lil' Gum Shoe" pop-up book about a young girl detective trying to track down her missing father: a book written for an audience of one.
Olive settles in at the nunnery and gets a new pet: Pigby the Pig.
At the Pie Hole, Chuck appreciates her new home, but she and Ned are unaware that Chuck's father is in the diner, watching.
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