Chuck was at her father's funeral while Ned was at his father. After their parents' deaths, Ned embraced pie-making and Chuck took up bee-raising.
Ned is helping Chuck by removing his clothing. Chuck obliges by stripping down to her underwear as well out of fairness. Her bees on the rooftop have died in a pesticide accident. Ned admits he hasn't seen his dad in 20 years and will stick with bees. Chuck then pours her dead bees all over Ned, while nearby an equal number of water bugs die.
Meanwhile, Olive is feeling uncomfortable with the secret that she knows Chuck's secret, and that she's still in love with Ned. And Emerson is working on his pop-up books about "Lil' Gum Shoe" when a prospective client comes in and says that his wife was having an affair and died in a work-related "accident." The husband, Dusty Fitz, isn't sure who his wife was leaving, him or the man she was having an affair with. He was eavesdropping and couldn't tell for sure.
Kentucky Fitz was the Number One Bee Girl of Betty's Bees, a famous honey-based company. She was stung to death behind the wheel of her Bee Mobile. Emerson, Ned, and Chuck go to the morgue and interrogate Kentucky, who is covered in bee stings. Kentucky insists there was no romance and she was leaving the company. She didn't tell Dusty because she didn't want him to worry that she was sabotaging Betty's Bees because Betty had it coming. She didn't see the murderer's face but he spit something at her and bees swarmed her. Ned makes Kentucky dead again just after she sabotaged the bees with a "lot of might." Ned is creeped out by the story. A swarm of bees emerge from Kentucky's mouth and they make a hasty exit.
Back at the Pie Hole, Ned is still creeped out by the bees. Emerson says they need an undercover agent at Betty's Bee and finds an ad in the paper. She interviews with Woolsey Nicholls, a former rival of Betty's Bee who bought out the company. Chuck raises the fact of Kentucky's death and the fact she was leaving, but Woolsey denies it and says their new brand relaunch was based on Kentucky's face: he's phasing out Betty because she's too old. Woolsey hires Chuck, while Emerson and Ned listen in on a bee bug. Chuck then searches Kentucky's office and finds a key in the desk. She also discovers Betty Bee in the wardrobe. Betty demands an explanation and grabs the key from the desk. She leaves and goes to her office and Chuck follows, but is ordered out.
At the Pie Hole, the team figures that both Woolsey and Betty have motives, while Olive wonders if Betty and Kentucky had a romantic relationship. Chuck is preparing pies for her aunts with the "special ingredient," and Olive notices it. Olive remembers how she discovered who Chuck's mother is, and Lillian banished her from the house. Chuck insists on investigating things further but Ned objects. They're interrupted when Vivian and Lillian come in. Chuck makes a hasty exit and Vivian wonders why Olive stopped delivering pies. Lillian was unable to stop her to come to the Pie Hole. Olive makes a feeble excuse and steps out to grab a pie. She then insists on explaining everything… and instead screams at the top of her lungs. Sick of the whole thing, she quits and Lillian offers Olive a place to stay.
The next day, Ned and Chuck go over Olive's now-deserted room and Chuck blames herself for Olive's departure while preparing to go to work. She admits to Ned that she was drugging her aunts to get them out of the house, but is happy she has her first job. Chuck wants to move out of Ned's room and into Olive's, upsetting Ned.
Meanwhile, Olive is on a mountaintop singing and dancing… at a nunnery.
Woolsey brings Chuck to see Betty. After Woolsey leaves, Betty explains that Woolsey obtained the company in a hostile takeover and her bee colony died. Chuck realizes that Kentucky sabotaged the hives using mites, not "might," but Betty insists that it was simply an accident. She grew up bees at her home, which she describes as her Honey House.
At the Pie Hole, the trio meets with Dusty and explains what they've discovered. They also explain that Kentucky sabotaged the hives, leading to her death. Dusty notes that Kentucky and Betty were like sisters until Kentucky was chosen as the new Bee Girl. Chuck assures Dusty that at least he knows that his wife loved him, but Emerson refuses to let him cry in public. Chuck assures them she can find the key the next day, but Ned doesn't say anything about the danger: he insists that it's Chuck's life. However, he spots Vivian outside and has Chuck hide, then goes outside to claim the shop is closed. Vivian says Lillian is gone and she didn't know where else to go. Ned suggests that Vivian move on, and considers doing so himself.
At the nunnery, Olive discovers that she has to give up her belongings to the poor and would like to be poor in other ways. The Mother Superior assures her she may come to want to stay, and assumes that Olive is pregnant. Olive quickly corrects her misconception, and the Mother Superior explains that Lillian came there to give birth to Chuck. They're interrupted when the poor arrive.
At the company, Chuck goes into the office to find that Ned is there: he's taken the place of Betty's assistant after tainting his pie. Chuck admits she feels safer already. Betty leaves and has Ned follow her on her last appointment, while Chuck breaks into Betty's office and gets the key. She notices a photo of Betty as a child with a bee beard… and turns to see a figure covered completely in bees.
A few minutes later, Emerson and Ned come in to find Chuck covered in bees but remaining perfectly still to not disturb them. Ned pushes her to the window and Chuck spits out a small container: the bees go out after it. As it turns out, the bee figure spit a container with the queen into Chuck's mouth and they nested on Chuck, who remained calm. Seeing the photo, they suspect that Betty Bee is the bee figure. Chuck also notices that the key matches the house in the background of the photo.
Olive goes to confessional only to discover that Lillian is there as a nun to make sure Olive doesn't leave. Lillian explains that Chuck's father was Vivian's fiancé so Lillian can never let Vivian find out. Lillian points out that Olive is having man troubles and the nunnery would be the best place to sort things out. Olive agrees but wonders how long Lillian intends her to stay.
Ned, Chuck, and Emerson don protective clothing and approach the house, Betty's childhood home, which they discover has become home to an enormous swarm of bees. They figure Betty and Kentucky conspired to steal the bees and fake the colony's theft to sabotage Woolsey's purchase, then brought them to the house. Betty is there and condemns Woolsey for producing inferior product. She refuses to let Woolsey have the bees, and insists that Woolsey killed Kentucky. However, if she explains to the police what happened then she'll go to jail even longer. She suggests they need DNA evidence to convict Woolsey independently of her testimony.
The trio takes Betty to confront Woolsey. As it turned out, French was in love with Kentucky but discovered the mite-infested bees and realized she was a saboteur. He used the queen bee and its container to kill Kentucky for revenge, and left his DNA on it via spit. Woolsey went to jail, never learning that Betty faked the bee colony collapse. Betty brings on Dusty as a partner and starts the Honey House.
Ned sets up Chuck's apartment with all of her belongings from Chuck's old room, and accepts that she'll still be with him. Emerson works on a pop-up book about Lil' Gum Se, a young girl who searches for her missing father. Olive is making a new friend: Pigby the Pig. And in the Pie Hole, Ned's father lurks, unseen and unknown.