Each chapter is headed by an excerpt from manuals on bees that parallel the action in the story. The quote preceding chapter 1 mentions the queen bee as the unifying force of the community. This sets the stage for the story of Lily Owens, age fourteen, and how the loss of her mother at age four fragmented her life.
The story is set in the summer of 1964 in Sylvan, South Carolina, where Lily is living on a peach farm with her abusive father, whom she calls T. Ray, and her African-American nanny, Rosaleen. She recalls the day her mother died in 1954, remembering few details--the suitcase on the floor, the fight her parents had, the gun that she picked up and accidentally set off. The police inquiry calls it a tragic accident.
Lily recounts her misery at school where she has few friends and only the encouragement of her English teacher, who tells her she is smart and should write. She thinks she is unattractive. Her father cannot help her with her adolescent issues, so she turns to Rosaleen, a surrogate mother.
Lily's longing for her mother is like a mystical religion. She has saved relics from her mother's things: a photograph, a pair of gloves, and a postcard of a Black Madonna (the Virgin Mary depicted as an African-American woman) with the place, Tiburon, South Carolina, written on the back. These are buried in a tin box in the orchard. When T. Ray catches her sleeping in the orchard with her box, he punishes her by making her kneel for hours on grits as sharp as ground glass.
That summer, President Johnson signs the Civil Rights Act into law, and Rosaleen walks to town with Lily to register to vote. Rosaleen gets in a fight with some Caucasian men hassling her and is beaten and thrown in jail for stealing fans from the local church.
The head quote, concerning swarming bees, who leave the old nest and settle nearby to start a new colony, foreshadows Lily's running away from home. Lily and Rosaleen are put into jail, but Lily's father gets her out and leaves Rosaleen there. Lily begs T. Ray to get Rosaleen out too, but he says she is in big trouble, and the man she insulted might kill her. In an argument, T. Ray tells Lily that her mother didn't love her; she was leaving the day she was killed. Lily is in shock. When her father leaves the room, she stares at a jar she left open, hoping the captured bees would fly away. They are gone, and she hears a voice in her mind saying that her own jar is open too. She gathers her things and leaves quickly, catching a ride to town with the church minister. He is on his way to press charges against Rosaleen for stealing the church fans.
When Lily finds that Rosaleen is in the hospital because the Caucasian men came into the jail and beat her, she goes to the hospital and helps Rosaleen escape. The two hitchhike to Tiburon, South Carolina, chosen because it is the only hint Lily has about her mother. She has a mystical vision of Rosaleen as a kind of Black Madonna when they bathe naked in a creek in the moonlight.
The bee headnote is the instruction for finding the queen bee: first locate her circle of attendants. Lily wakes up by the creek where she and Rosaleen have spent the night. She calls this day one of her new life. They walk to Tiburon and buy some food at the general store. Lily discovers her mother's picture of the Black Madonna on some jars of honey and asks about them, thinking it is an omen. The storekeeper tells her the honey is made by August Boatwright, a colored woman, and explains how to find her pink house. Walking through Tiburon, they see signs of the times: a sign about Goldwater for President and a bumper sticker supporting the war in Viet Nam. Lily buys a newspaper looking for news of their escape, but it is only full of news of Malcolm X, Saigon, and the Beatles.
Each colony of bees is a family unit, explains the bee headnote. Lily and Rosaleen meet the Boatwright sisters, August, May, and June, African-American women who live on the edge of town on a bee farm. Everything in the large house is rubbed down with beeswax, including the black wooden figure in the corner whom Lily instinctively identifies as a Black Madonna. She feels a magnetic pull to it. Lily makes up lies about why Rosaleen has stitches in her head and what they are doing there. She says her parents are dead, and she is on her way to live with her aunt in Virginia. She asks if there is any work for them so they can earn some money. August says Rosaleen can help May in the house, and Lily can help with the bees.
When May starts to talk about her twin sister April who died, she begins to hum "Oh! Susanna," a distress signal to the other sisters that May is about to go on a crying jag. They send her outdoors to her wailing wall to calm down. The sisters make the refugees at home and give them sleeping cots in the honey house, a garage/factory. Even though Lily has never felt so white, surrounded as she is by African-American women, she feels she belongs in this house. Lily makes Rosaleen promise not to tell about the picture of the Black Madonna. The only strange thing is May's homemade wailing wall with its little bits of paper stuck in the stones, carrying names of the African Americans killed in civil rights demonstrations.
The headnote speaks of the darkness of beehives. The first week at August's is a relief in Lily's life. August asks no questions but helps the visitors settle in. Lily is trained in beekeeping, as Rosaleen helps May with the cooking. May is oversensitive to suffering and will not even kill cockroaches. June is a history and English teacher at the African-American high school and plays the cello for dying people. Lily overhears June telling August that they should not have taken the strangers in; everyone is aware Lily is lying. June dislikes Lily because she is Caucasian, and this reverse racism surprises Lily. The soothing fatherly figure of Walter Cronkite giving the news on TV is the opposite of T. Ray in Lily's mind. When, however, Cronkite reports the racial violence that summer, May has a fit. Every night the family kneels before the Black Mary, called Our Lady of Chains.
One evening August tells Lily a story of the nun Beatrix who ran away from the convent. When Beatrix finally returned, humbled, she found the Virgin Mary had stood in for her all those years, so people wouldn't know she was gone. Lily realizes August is trying to tell her something about her own situation, and after that, she begins asking the Virgin Mary for help. August teaches Lily bee etiquette and how to send them love so they won't sting. Lily wants August to love her, so she will keep her. August tells Lily about May's sensitivity stemming from her twin sister's suicide at fifteen when she discovered the suffering of African-American people. At night, Lily longs for her mother. She senses her mother has been here, but Rosaleen warns her, what if Lily finds out something she doesn't want to know?
The queen bee produces queen substance that attracts the other bees, announces the headnote, introducing the chapter on Our Lady of Chains. Lily meets Neil, the principal of the African-American high school, who wants to marry June. She won't have him, because she was jilted once before at the altar. Lily and June have a private war. On Sunday the sisters host a religious meeting, called the Daughters of Mary. These are local African-American women who show up in colorful costumes that Lily loves to look at. They say Hail Marys, and August tells the story of Our Lady of Chains, as follows.
The statue was once a figurehead of a ship washed up and found by slaves. She looked like a Black Madonna with her fist raised. The slaves believed she had come to give them freedom and worshipped her. She was so powerful, the master hauled her off and chained her up, but she miraculously made her way back to the slaves fifty times without help, until the master gave in and let her stay there. One by one each Daughter of Mary touches the heart of the statue, and Lily longs to touch it too, but June stops playing the cello at that moment, as if to say, you aren't one of us. Lily faints. Walter Cronkite announces the plans for the first moon launch on TV, and August tells Lily this is the end of the moon's mystery. (The moon is where Our Lady lives.)
The headnote wonders how bees ever became associated with sex. This introduces Lily's meeting with Zach, the teenage African-American boy who helps August with the bees. Zach surprises her by being smart and handsome. He becomes Lily's best friend. Her only problem continues to be June, who is constantly hinting it is time for Lily to be leaving. Lily tells Zach about her love of writing, and he explains he wants to be a lawyer. She has never heard of an African-American lawyer, but Zach tells her you have to imagine what has never been. Rosaleen teases Lily that she is living in a dream world, trying to make this their home. Lily wants to confess everything to August but is afraid she will be sent back to her father.
When Zach and Lily are out on the truck driving around to beehives, Lily begins to be attracted to him. This frightens her because of the racial difference. They visit Mr. Clayton Forrest in Tiburon, the Caucasian lawyer who has befriended Zach. Zach tells Lily about the famous local writer, Willifred Marchant, and Lily is defensive about her own desire to write. He comforts her when she starts to cry, and she puts her head on his shoulder. August tries to help Lily feel comfortable enough to open up, but Lily holds back. Neil and June have a fight and break up. Lily finds herself falling in love with Zach. When he gives her a notebook for her stories, they embrace and remark on how dangerous their affection is. Lily writes stories that feature Rosaleen and August and Zach as heroes.
The bee headnote says that if a honeybee is isolated from her sisters she will die. Lily settles in to her new life with the Daughters of Mary. August becomes her teacher, showing her the beekeeping business. Lily imbibes a new culture that stems from the Black Madonna, the legacy of the Boatwright grandmother, Big Mama. August tells Lily that Mary is everywhere, inside everything. When Lily asks about her history, August says that both she and June graduated from a Negro college. When August could not get a job, she became a housekeeper in Virginia. Then she inherited the bee farm from her grandmother. She never married because she prefers her freedom.
August shows Lily the beehives and tells her bees have a secret life. If she doesn't want to get stung, she must give love to the bees. Lily has another of her mystical experiences with the bees. She feels they are greeting her as a sister, trying to comfort her. In Tiburon, the racial climate is tense as the movie star, Jack Palance, plans to come to town and integrate the theater by taking an African-American woman with him. Lily remembers the Northerners coming down on a bus in her town to integrate the city pool. Lily wonders why God made different skin pigments. Lily goes with Zach to deliver honey in Tiburon to the lawyer's office. Lily makes a collect call from there to her father, hoping he has missed her. He begins yelling at her, and she hangs up. When Lily gets home, she writes a letter to T. Ray accusing him of being a bad father but tears it up. At night when everyone is asleep, Lily goes to Our Lady of Chains and prays to be fixed.
The bee headnote mentions that the fabric of bee society depends on communication, implying a lack of it will be the theme of the chapter. Lily says that July 28 was a day for the record books. While Ranger 7 lands on the surface of the moon, and the police look for the bodies of dead civil rights workers, Lily and August water the bees with sugar water because the temperature will be over one hundred degrees that day. Lily gets stung on the wrist by a bee, a sort of initiation into beekeeping. May, Rosaleen, August, and Lily play in the water sprinkler, getting soaked. When June comes out, Lily soaks her with water, and they have a water fight, ending in laughter and forgiveness. Lily and June hug. Lily feels she should tell August about herself but is afraid to spoil the happiness she has found. When she sees May making a trail of graham cracker crumbs and marshmallows to get the roaches out of the house without killing them, Lily is startled, remembering her mother did a similar thing. She wonders if her mother had been here. She asks May if she knew a Deborah Fontenel. May says yes, she stayed in the honey house.
Just as Lily decides she needs to talk to August about her mother, Zach asks her to come to town with him. They see trouble happening between a group of colored boys and some white men. One of the black boys throws a bottle, and the glass cuts a white man. All of the boys are arrested, and no one will say who did it. Zach will have to stay in jail for at least five days before bail can be set. Everyone is angry and worried for Zach, and they decide to keep the news from May. August and Lily visit Zach in jail. Lily promises him that she will write all of these events in a story for him. A few days later, the phone rings and May answers it. It is Zach's mother, who tells May the boy is in jail. May collapses. Then she says she is going to the wailing wall. It is dusk. May takes a flashlight and goes out alone.
The headnote concerns the shortness of a bee's life. When May is delayed returning from the wall, everyone sets out to find her. They comb the woods while June calls the police. August finds May in the river in two feet of water with a stone on her chest. Lily is nauseated and vomits in the wood. August tells the policeman that May was depressed. He questions Lily, and she lies about who she is and what she is doing there, saying she is an orphan. He does not understand why a Caucasian girl is staying with African-American women and tells her she had better not be there when he returns.
Lily dreams about Zach, but when she wakes, she remembers he is still in jail. The coffin with May in it, fixed up, comes home to the pink house, so May can be mourned properly by the Daughters of Mary. June plays the cello, and Lily feels May's presence in the room. She speaks to her, asking her to look up her mother in heaven with the message to send a sign to Lily that she loves her. Zach arrives, having been let out of jail, and Lily sees something in him has changed.
August, Lily, and Zach go out to drape the hives with black crepe. If the bees stay in the hive, it means the person will live again. August says there are pictures of bees scratched on the walls of catacombs as a symbol of resurrection. When the Daughters of Mary come for the vigil, they make Lily feel like one of them. Lily thinks African-American women are like hidden royalty and doesn't know how they had become so low on the totem pole. May's suicide note is found and she explains to her sisters that she is tired of carrying around the weight of the world. She is going to lay it down. She asks her sisters to live. August tells June it means she must marry Neil.
The bee fact announced at the beginning of the chapter is that it takes millions of foraging trips to make one pound of honey. This chapter brings together the bits of happiness the characters have earned between them all summer. Now Lily is desperate to have her talk with August about her mother, but August is in her period of mourning and keeps to herself. Neil and June are courting, and Lily and Zach keep company. She wishes she were a Negro girl, but he says they can't change their skins, only the world. He still dreams of being a lawyer. Zach has an angry edge to him now; he speaks of racial tensions and Malcolm X.
When the mourning is over, there is a celebration dinner and evening prayers, and Lily feels the world is back to normal. Lily prepares herself to talk to August about her mother, but she is afraid of being sent to prison for her crime of helping Rosaleen escape. The talk is put off once more, for it is Mary Day the next day, and everyone is baking and decorating. It is a day of thanks when the story of Our Lady of Chains is reenacted. Neil asks June to marry him again, and she says yes. They go off to buy her ring. The Daughters of Mary arrive in the evening and fuss over Lily. They form a circle of feeding and give each other a sort of communion of honey cakes. The statue of Mary is hauled in the wagon, and chained in the honey house for the night as part of the ritual.
Zach and Lily go for a walk by the river, and she asks him not to become mean in his anger at the world. He kisses her. He says he will do everything to become a lawyer, and Lily knows he will, because changes are coming, even to South Carolina. He promises after he makes something of himself, they will be together. He gives her his dog tag.
The headnote explains the behavior of the queen bee, shy and skittish and perpetually in eternal night, the mother of the hive. This is a chapter about August and Lily's mother, Deborah, the mysterious queen bees of the story. Lily waits in August's room. When August enters, Lily lays out the picture of her mother and asks if they can talk now. August knows who her mother is and says Lily is the spitting image of Deborah. August tells her she worked for the Fontanel family in Virginia and took care of her mother when Deborah was a little girl.
Lily explains why she left home and cries in August's arms. August is like a sponge, absorbing her pain. Lily confesses how she accidentally killed her mother. August tells her that in spite of that, Lily is lovable, and that it seems she was meant to find them. August explains Deborah's background and painful marriage to her father, who was not always so mean. In the beginning, he worshipped her mother and was desolate when she left him. Deborah only married because she was pregnant, and when she felt trapped, she turned to August as a mother, the way Lily turns to Rosaleen. She fled to August's house in Tiburon when Lily was small, because she was falling apart.
Lily says she now hates her mother for leaving her behind. Lily had created a myth about her mother's love, and now she faces the bitter truth that she was an unwanted child. August defends Deborah, saying she had a nervous breakdown, but after three months, Deborah went back home to collect Lily and her things and move to Tiburon. The accident prevented that. August tucks Lily into bed and tells her that nothing is perfect; there is only life.
A worker bee can fly with a heavier load than herself, explains the headnote. Lily carries the weight of her discovery about her mother in this chapter. The statue of Black Mary is still bound in chains in the honey house, but Lily approaches her for help. She wants someone to understand her devastation and anger at losing her mother. In a fit of anger she flings all the honey jars against the wall and smashes them. Emptied out, she falls asleep by the statue. Rosaleen finds her with blood on her arm, then cleans her up as Lily explains her anger. Lily realizes she could allow this bitterness to take over her life. Rosaleen and Lily clean the honey house before the Daughters of Mary come for the end of the Mary Day ceremony, celebrating Mary's Ascension to heaven.
Neil and Zach unchain the statue and put her on the ground in the sun. They take off her chains, read the Bible, and bathe the statue with honey. This ritual with the other Daughters has a healing effect on Lily. Lily thinks to herself if she could have one miracle from the Bible happen to her it would be to be raised from the dead. August brings Lily a box of her mother's belongings. Among the items is a photo of Deborah with her baby, Lily. Their noses are touching and her mother smiles radiantly. This is the sign of love from her mother that Lily had been looking for.
The headnote announces that a queenless bee colony will die, but a new queen can be introduced to make great change. This comments on Lily's own healing and acceptance of her divine mother, Mary. Lily spends time by the river. She muses over all her hurts and is haunted by her mother. August says she is grieving. Meanwhile, June plans her wedding to Neil, and Rosaleen goes to town to register to vote, to finish what she tried to do in Sylvan. Then Zach announces he is going to the Caucasian high school in the fall. Life goes on.
Lily cleans her room and makes an altar with her mother's things. She has finally made her peace. The next day she wears her mother's whale pin on her dress. Her mourning is finished, and she goes to the beehives with August. One of the hives is missing a queen. August explains they have to put in a new queen to save the hive. She also makes the connection to Lily's situation. If her own mother, Deborah, is missing, then Our Lady could be the stand in, she suggests. August says that Our Lady is not outside but inside of us. August takes Lily's hand and places it on her own heart.
T. Ray, who traced her from the collect call from Mr. Forrest's office, finds Lily at the Boatwrights. She is alone. T. Ray takes out his knife and stabs the chair in a threatening way, saying he will take Lily back. Then he sees the whale pin on her dress and is shocked, for he had given it to Deborah. Lily finally sees how much he must have loved Deborah. T. Ray hits Lily so hard, she falls into Our Lady. He starts calling her Deborah, as though temporarily mad, and she calls him Daddy to snap him out of it. Lily feels she has seen into the dark place in his soul that will never heal. She asserts that she will stay with August. August comes into the room and confirms they love Lily and want her to stay. The Daughters of Mary arrive to stand by Lily, and T. Ray leaves. As T. Ray is pulling out in his truck, Lily runs to ask him if she truly killed her mother. He says that she did, and that it was an accident. She doesn't know if he tells the truth, but she turns back to all the loving women on the porch waiting for her. Clayton Forrest has the charges dropped against Lily and Rosaleen. Lily becomes friends with Clayton's daughter, Becca, and they enroll in the same high school with Zach. Lily continues to write her stories and takes over May's wailing wall, feeding it with prayers. Often she feels Black Mary inside, rising up, filling up the holes life gouges out.