The story tells about one summer of a fourteen-year-old girl named Lily Melissa Owens, the summer that changed her life. Lily lives with her father, who is a widower, on his peach farm and at first she seems to be an ordinary, though unpopular girl. She is quite lonely in her small town of Sylvan, Carolina, and the only beings that she can truly consider friends are bees that fly into her room at nights. That’s strange, and her father named T. Jay, whose attitude changes from ignorant at worst to outright abusive at best, doesn’t believe that bees visit Lily every nights. This stories makes him angry and he uses them to mock Lily. Lily’s nanny, Rosaleen - a woman who T. Jay hired to substitute his deceased wife in housekeeping and babysitting - does believe though. Or she just says so not to disappoint Lily, who depends on her stories very much.
The novel starts when Lily lies in her bed waiting for bees to return to her. She thinks about her mother and from her thoughts we learn that the girl suffers from guilt for her mother’s death. Lily’s mother, Deborah, died when the girl was only four. The girl’s memories about that day are scarce, but she vaguely remembers that her parents were arguing and she did something to stop the argument. Something that included her mother’s gun in her hands. Lily is sure that she just picked up the gun when Deborah dropped it and remembers that it accidentally fired, but T. Jay says that it was Lily who killed Deborah, she shot her. Lily is not sure whether her father lies to her to make her more obedient and just hurt her or she is indeed her mother’s murderer. But this dark secret and horrible thoughts about it alienated her from the world completely. Rosaleen managed to warm the girl up towards her by her persistent tenderness and compassion, but still Lily remembers her mother very well and misses her so much.
In the meantime, Rosaleen watches the TV. More specifically, the broadcast of the current President Johnson signing the Civil Rights Act. Rosaleen, as a proud black woman, feels obliged to go to the town centre and vote for it. In the next day she offers Lily to accompany her and the girl agrees. But when they are walking towards the centre of the town, passing the gas station nearby, three white men surround Rosaleen and start harassing her right in front of the girl. At first the whole thing is verbal and the woman stands for herself quite well. But soon the men get too angry to limit themselves to words only and they try to assault her physically. Rosaleen fights back, but when the police arrives it is she and Lily who get arrested and transferred to the jail just for the mere attempt to defend themselves. The Civil Rights Act is indeed needed.
Soon T. Jay comes, but it’s only Lily who is taken away from the jail. The man doesn’t care about Rosaleen who lived in his house for ten years, looking for his daughter and doing his laundry. Moreover, at first he scolds and harshly berates Lily for helping Rosaleen, calling it a stupid and senseless behaviour and then he makes her even more guilty saying that those three men will most likely kill Rosaleen for being not obedient to their wishes - if she isn’t already dead because of the injuries - and Lily in a way helped them to make this decision. So she is twice a mother killer in a way.
Lily is devastated. But the example of Rosaleen inspires her and she starts an argument with her father, defending her position and calling him out for being so abusive and manipulative, for lying to Lily about her always making things worse. In response T. Jay tells Lily even more horrible thing for the girl: her mother decided to abandon her that day when Lily shot her. The argument had to be the last one before the divorce, but Deborah’s daughter ended it her own way.
Lily doesn’t believe a single word. Her father accused her of everything and made her life miserable too much to take that too. She leaves to her room, but now the girl is filled with cold determination to save Rosaleen from the prison. When she enters her room she sees that her bees have escaped the jar they lived in. So the girl decides it is a sign: she must not only help Rosaleen escape but also run away with her, as the bees did. Before she goes to sleep, she takes the only thing that is left to her by her mother: a picture of Black Madonna with the address on its back: Tiburon, South Carolina.
The next day, when T. Jay is away, Lily packs her belongings and some of her mother’s in a bag and comes to visit the hospital where Rosaleen stays after the beating. She discovers that the police officers had beaten her too (and possibly did something even worse). But still the woman is capable to walk, so the girl helps her to escape. Rosaleen is shocked and mildly annoyed that Lily broke the law just to follow a vague trace of her deceased mother, effectively going to nowhere, but the girl feels as free as never before and determined to find any information about previous Deborah’s family, with Rosaleen or without her. Of course the woman can’t leave Lily alone. Together they go to the highway and hitchhike to Tiburon. The travel goes smooth, though it was extremely dangerous for a black woman and underage girl to travel that way during those times. Finally Rosaleen and Lily arrive to Tiburon.
But from now on they don’t have a clue about the direction. They come to a local shop to buy something to eat and accidentally see honey jars with the same picture of Black Madonna on the etiquettes. Lily thinks it is a trace. She asks the owner of the shop about the origin of this honey and gets the address of an apiary nearby. The farm belongs to the Boatwrights family - the three black sisters with very appropriate names for the beekeepers: May, June and August. Rosaleen and Lily travel there to meet the owners of the apiary personally.
August - who is the oldest of the sisters and the owner of the apiary - welcomes them without any extra questions. Despite Lily quickly comes up with a not very plausible false story about why they are here, August just doesn’t care. But June does. She is very suspicious to both newcomers and is not amused at all when August gives Lily a job at the apiary and offers Rosaleen to keep their house. Rosaleen returns to her duties of a nanny too: the third sister, May, is so oversensitive that she should be nursed sometimes. May is compassionate and kind, but sometimes she is so overwhelmed with sad thoughts that she has to write them out of her head and stick the papers to her personal “wailing wall”: a stone wall of the farm with lots of cracks in it. The suicide of June’s twin sister, April, shook her mind too much and May is still recovering from such a deep trauma.
Another person who visits the apiary often is Neil, June’s boyfriend. They are together for many years and Neil proposed to June several times, hoping to take her to their own home and start a normal life (from the society’s point of view). But June, though loving him, keeps rejecting the proposal: she likes her apinary and her independence more. As we discover later, there is another thing she values: being a member of a women-only secret society.
This secret society is called the Daughters of Mary. The women come to the “honey house” to pray to the Black Madonna. Their religion is based on Catholicism with all the key rituals (reciting the Rosary, praying to Virgin Mary), but it is heavily influenced by the native African religion. The women ask Mary to help them be strong and to break social barriers that restrict them. The prayers and gatherings work also as a group psychotherapy where the women support and help each other. To her surprise, they don’t treat Lily as a white or as an underage girl. The Daughters of Mary accept both Lily and Rosaleen as equals, open-heartedly and without demanding anything back.
Lily gradually gets along with everyone on the apinary including Zach, a black boy of roughly her age who also helps with the bees. She is given her own room and starts to value all the farm inhabitants as her own new family. Lily is especially attached to August who became her another mother substitute, but she still afraid to tell her the true story about why she and Rosaleen came here. The girl fears that after hearing that Lily possibly killed her mother and broke the law, August will reject her and send her away. The things become even more complicated when Lily understands that she developed a romantic (and mutual) relationship with Zach, but it is doomed - the couple of the white girl and black boy would not be tolerated by society.
Lily and Zach spend lots of time together, sharing their dreams and thoughts. Lily tells him that she wants to become a writer and Zach answers that he dreams to be a lawyer someday. She is too shy about it and, trying to cheer her up and encourage, Zach presents her a diary to note her thoughts and practice in writing. Grateful, Lily accompanies Zach to the town, helping him to deliver honey to one of the lawyers. The man is white, but he believes in Zach and takes him as his unofficial apprentice, allowing him to come to his law office and learn. While Zach and the lawyer go away to talk for a while leaving Lily alone in the office, she sees a phone and, feeling an outburst of anger, calls her father, asking him if he ever knew her favourite color. T. Jay expresses nothing except anger too, shouting at his daughter and promising to find her, take home and heavily beat. Lily aborts the call. The care and compassion of the women and Zach contrasts so much with her previous life.
One morning Lily sees May in the kitchen doing something that she remembers her mother doing. Carefully, she asks May about Deborah and the woman replies that indeed she knew her. Lily is shocked by this discovery. She stops interrogating May to not shake her fragile senses, but the girl can’t make herself to confess to August also. So she decides to wait a bit more. Soon she and Zach drive to Tiburon again - Zach needs to buy some spare parts. But while they are parking, some black teenagers throw a bottle into a white man. The police that arrived catches all the black teenagers around, Zach included - not even trying to sort everything out. Like in Rosaleen’s case, if you’re black you’re guilty, period.
Lily returns home. The women are deeply worried about Zach but they still try to keep calm, so May won’t know anything. They tell her some story about why the boy is absent. But unfortunately, while Zach calls home from the jail, May is the one who answers the phone and the poor woman learns everything. She doesn’t tell anyone, but at night she is so exhausted by her depression and bad thoughts that she leaves the house secretly and commits suicide by drowning in the river nearby, following the path of April.
All the next week the family is busy with the funeral. The other Daughters of Mary come to their house to help and mourn May together. When it’s over, Zach returns home, unpunished. It seems that his law studies were very helpful. But it’s too late for May…
While cleaning the room of May June finds a note left for her. May urges her to enjoy life, unlike she did, because life is too short to fill it with constant sorrow. June thinks it over for a long time and finally decides to marry Neil. They set a date for their wedding. Lily also finds courage to proceed in her relationship with Zach - they finally kiss on one of the dates and promise to each other to be together one day, openly, despite their different races and social prejudices. This is not the only thing Lily gathers her willpower for. She finally talks to August about the real causes of her coming to the apiary and about her mother Deborah.
The story of August devastates the girl. At first August tells that she always knew about Lily’s origins, because she looked too much like her mother. Debora once was a housekeeper and nanny in Deborah’s house. She saw all her life and her marriage to T. Jay, her unhappy life and nervous breakdown after giving birth to Lily. August confirms the very worst thing T. Jay told his daughter about her. Deborah indeed divorced and abandoned Lily. The day they argued with T. Jay and Deborah was killed she returned only to pick up her possessions. Shocked and angered, Lily tells August that it was she who killed her mother, but August just asks her to forgive both herself and Deborah for being just humans and not perfect beings. Lily closes herself in her room, mourning the ideal image of her mother that was shattered. She is able to overcome her grief only days later. She thinks over the August’s words and agrees with her. During the next talk, August transfers to Lily some of Deborah’s possessions including a photo of her feeding her little daughter, Lily. This photo becomes a long-awaited manifest of love and forgiveness for the girl.
But when everything seems to return to normal, T. Jay appears on the horizon. He has finally tracked his delinquent daughter and now is eager to take her back home whether she wants it or not. Lily doesn’t want to go, they have an argument again and T. Jay hits and kicks her, trying to force her into the car. Suddenly Lily has a moment of understanding and she tells him that she is not her mother, she is a separate person. This hits home. When Deborah left, T. Jay was so angered and offended that he transferred his feelings to Lily, who looked so similar to her mother. He mocked her and psychologically abused trying to take revenge on deceased Deborah.
But now Lily is confident and strong enough to forgive him and even call him “Daddy”. August asks T. Jay to leave the girl with them and after a moment of hesitation the man agrees. Before he leaves, Lily asks him if she really did kill her mother. T. Jay says yes - but than, for the first time in her life, he adds that she is not guilty and it was a tragic accident. Finally Lily knows the truth, but now she can withstand it and forgives herself.
In autumn, Lily and Zach go to the same school. Now she is popular among her classmates. This summer has changed Lily a lot: from a perpetually sad, alienated and guilt-ridden girl she matures into a confident young woman who loves herself and has the strength both to defend herself and to forgive those who did wrong to her.