How It All Goes Down
Our narrator, Lily Melissa Owens, spends most of the book describing events that took place the summer she turned 14. When the story begins, she's a lonely and unpopular teenager living in Sylvan, South Carolina (it's fictional—put your map away). She suffers mightily from an unhappy home life; her mother died when she was four, and her father, T. Ray, is neglectful on his best days and abusive on his worst.
Lily has a good relationship with Rosaleen, the woman charged with taking care of her, but she nonetheless yearns for her mother. We quickly learn that Lily accidentally played a role in her mother's death; she got in the middle of a fight between her parents, picking up and accidentally firing a gun that had dropped to the floor in the commotion. She barely remembers the incident, but it's clear she feels a lot of guilt about it. And of course, she misses her mom, too.
On her birthday, Lily decides she's going to accompany Rosaleen into town. When they get there, Rosaleen gets into a verbal sparring match with some white men outside a gas station that eventually gets physical, and the police are summoned. Rosaleen ends up charged with a number of things, and she and Lily get hauled off to jail. T. Ray comes and gets Lily, but Rosaleen has to stay put.
Then T. Ray and Lily get into an argument where T. Ray grows angry enough to reveal that Lily's mother had abandoned Lily when she left T. Ray just prior to her death, a tidbit that Lily had never heard. Reassuring herself that T. Ray is just lying to hurt her, Lily decides to run away—and bust Rosaleen out of jail in the process.
After successfully sneaking Rosaleen out of police custody, she decides they will go to Tiburon, SC, because that location was written on the back of a picture that had belonged to her mother. It's a very unique picture, an image of a black Madonna.
When she gets to Tiburon, it doesn't take her long to figure out the Madonna's origins; in the general store where she stops to grab lunch, she finds honey jars with that picture all over them. She is hopeful that finding the maker of that honey will lead her to people who knew her mother.
With a little further sleuthing, she quickly locates the address of the beekeeper who produced the honey, August Boatwright. Lily and Rosaleen go straight to August's house (where August's sisters May and June live as well) and end up scoring an invitation to stay. Lily is not entirely forthcoming (er, that is, not really at all forthcoming) about her true reasons for being there, at least initially. August seems to realize as much but doesn't actually care; she just puts her two guests to work, Lily with the bees and Rosaleen in the house.
As time goes on, Lily gets into a good groove with the sisters and learns more about their rituals and traditions, including their Catholicism-infused (but not entirely Catholic—at least, in the traditional sense) worship of the Virgin Mary as part of a group called the Daughters of Mary. June is initially pretty suspicious of Lily, but they eventually become friends, too.
Lily befriends August's assistant, Zach, and the two soon develop lots of lovey dovey feelings for each other. However, Zach is black, which, given the political climate at that time, makes it too dangerous (in their view) to try to be together romantically. Lily becomes all too aware of the dangers Zach encounters in a post-Civil Rights Act, post-integration South when he is arrested during a tussle his friends and some white men who were camped out trying to prevent the local theater from integrating.
Zach's arrest has other repercussions as well. The ultra-empathetic May is so upset to hear about the situation that she commits suicide. The sisters, the Daughters of Mary, Lily, and Rosaleen are all devastated. (Zach is released soon after May's death.)
Eventually, Lily gets up the nerve to ask August about her relationship with Lily's mother, and she learns more about her mom's separation from T. Ray. She is upset to learn that her mother had, in fact, left her, as T. Ray had said. It takes her a while to get over the shock of this revelation.
Then, T. Ray tracks her down and shows up in Tiburon, threatening to take Lily home. She and August convince him to just leave her there, with August promising to take care of her. He consents and leaves.
With that and a few additional details, Lily basically brings us up to speed with her life so far. She is still in high school when the novel closes, and she claims to have found a good home with Rosaleen, the Boatwright sisters, and the other surrogate mothers that the Daughters of Mary (and the woman they worship) represent for her.