Lily is the main character, protagonist, and narrator of her story. She is a fourteen-year-old white teenager growing up in Sylvan, South Carolina. When Lily first appears, she is beaten down, abused, and misused by her brutal father. He runs a peach farm where Lily has always lived, and neither he nor Lily ever forget that at age four, Lily killed her mother while witnessing an argument between her parents. But within Lily are qualities she discovers only after she leaves home and goes on the run with her nanny, Rosaleen. Through her interactions with other people, Lily gains strength in her independence, understanding of prejudice, and loving connections in her life. Her sense of humor helps her survive, and she comes to an understanding of her yearning for her mother, her ability to forgive, and her growth that takes her far beyond her father's lack of humanity.
Lily has always been beaten down and abused by her father, but witnessing Rosaleen's courage gives Lily courage, too. Her father physically beats her and punishes her atrociously, and Lily has no choice but to take it. But after she witnesses Rosaleen's nerve in the face of beating and imprisonment, Lily finds her spark of independence and ingeniousness. She learns to lie convincingly and plans their escape to Tilburon. Defying her father and leaving home is something she'd never considered. She uses her intelligence — a brain that her father thought was a waste to educate — to create a false past, learn a new set of skills, and reflect on the people and events she sees around her. In the end, she even finds the courage to stand up to her father once and for all.
Racism is a fact in South Carolina, and although adults like T. Ray and Rosaleen know how dangerous it is, Lily doesn't know, and that danger will become part of her education. When T. Ray tells her that Rosaleen will probably die at the hands of racists, Lily takes no time to even question saving her. Later, although the television news tells Lily facts and shows her pictures, the incident with Zach in town is a stronger education. Lily realizes that the white world does not think she should live with the Boatrights and certainly would frown on any liaison with Zach. However, Zach encourages her to imagine a color-free world in order to make it happen. The lessons her father taught her about race are slowly proven wrong, and one notion after another falls. When Lily realizes June is prejudiced against her because of her whiteness, Lily is shocked and recognizes how wrong June is to judge her without knowing her. Once again, Lily reflects on this idea and takes it in.
Part of the reason Lily can survive, as one after another of these early lessons are shattered, is that she has a great sense of the absurd. She even has a conversation with God, asking why He couldn't stick with his "original idea about Paradise." Her sense of humor gets her through many situations, including her father's abuse — she muses that many children have a parent who doesn't love them but wonders why must she have two? Perhaps she developed her sense of the absurd to shield herself from pain.
Throughout her story, Lily feels a deep sense of longing for her mother and a need to connect with other human beings. She reflects on the mother she allegedly killed and compares herself to her unknown mother, always coming up short. She imagines her mother romantically, doing things ideal mothers do, like brushing Lily's hair. Lily goes to Tilburon in search of her mother, not knowing whether her mother had really been there. After August presents Lily with her mother's items, she finds the photo of her mother feeding her as a child, and all the longing and sadness of her life is contained in her reaction. Through August and Zach, Lily begins to find loving connections to humans who treat her like she is a human being. The teacher who first encouraged her began that connection, and Rosaleen followed it up. Now the Boatright home and sisters show her what it is to be part of a community who loves her. Zach also believes in her, giving her a journal for writing her thoughts. This group of people gives her the courage to stand up to her father.
In forgiving both herself and her mother, Lily becomes a better person than her father. All her life, she has accused herself and beaten herself up mentally for her mother's death. She also has been bitter and angry about her mother's leaving her. But in the end, Lily finds a way to forgive both her mother and father and, in doing so, she begins to see her father's bitterness and anger over being left by Deborah. Lily reaches out to him, but he can't see his own way to forgiveness. Being able to see his viewpoint is the final step in Lily's growing into a young woman who believes in her worth and can love others.