Prep is a coming-of-age novel describing Lee Fiora's high-school days at Ault, a prestigious New England boarding school, which she attends after an unremarkable, middle-class upbringing in Indiana. The book recounts her friendships, conflicts, and worries over the course of her time at Ault, and a thoughtful vein of social critique runs through it, questioning the school's social dynamics and culture. It is narrated by the adult Lee Fiora, speaking many years after her graduation from high school.
The first chapter takes place during Lee's first semester of high school. She feels desperately lonely, confused, and unhappy during this time. The catalyst for much of what comes next is a disastrous Ancient History class: Lee prepares her presentation on the wrong topic and runs out of class crying. As she flees, she runs into Gates Medkowski, a senior prefect and very popular student. Gates is kind to Lee and reassures her that her experience will improve. Gates' kindness prompts Lee to develop an obsession with her. She also encounters some of the other figures who will shape her school experience. Among them are her roommates, Dede and Sin-Jun, both of whom she will end up staying in touch with throughout her schooldays and into adulthood, but with whom she is not particularly close her first semester. She also develops a friendship with Little Washington, one of Ault's few black students, who, like Lee, is on a scholarship. However, their friendship is cut off when Little is expelled for stealing— a violation of rules which Lee herself discovers when she catches Little leaving her own room. Lee is forced to turn her friend in to the school, after a tortured decision-making process. Chapter One also clues us in to the process that brought Lee to Ault. Though, as she explains, her parents thought her preoccupation with boarding school was a mere phase, she unexpectedly got in and was offered a scholarship. As a result, she reflects, she has found herself in a situation she never truly expected to be in.
The second chapter takes place during the winter of that same year, when Lee feels slightly more settled but hardly any happier. Lee learns about a school tradition called "surprise holiday," in which all classes are canceled in the morning and students enjoy an unexpected day of freedom. She intends to spend her surprise holiday at school, but at her roommate's prompting winds up taking a school-hired bus to a nearby mall to get her ears pierced. After the piercing, Lee faints. She is discovered by Cross Sugarman, one of the most popular boys in her grade, with whom she has had almost no interactions before. Cross cares for her and spends the day with her, inviting her along to a movie and to wander the mall with two of his friends. Lee develops a crush on him over the course of the day, although she knows he is dating an older Ault student. Lee, Cross, and Cross's two friends share a cab back to school, and in the backseat Cross strokes Lee's hair, cementing her crush on him. They rarely speak for the next two years, but her attraction to him only grows stronger.
Chapter Three starts in springtime, when Lee finally finds deep friendship at Ault during lacrosse practice. A girl named Conchita Maxwell asks Lee to be her partner during practice. Conchita wears colorful clothes and seems to actively resist all of Ault's social codes. She is also so blunt that Lee feels both thrilled and uncomfortable around her—Conchita speaks openly about popularity and conflict in their class. She invites Lee to her lavishly decorated single room, where Conchita introduces Lee to Bob Dylan's music. Their friendship deepens over the next few months, with Lee teaching Conchita how to ride a bicycle. Conchita asks Lee to be her roommate sophomore year, but Lee privately feels hesitant. When Conchita's mother comes to visit, Conchita invites Lee to go to lunch in Boston with the two of them, as well as Conchita's other friend Martha. Martha and Lee bond that day, and ultimately decide to room together. Conchita is so devastated by this that she ends her friendship with them both. This plotline intersects with one about a schoolwide game of "assassin," in which students get one another "out" by attaching small stickers to one another. Lee excels at the game and even realizes she might win. She plans to stay in until the number of students is small enough that she will be forced to directly chase or be chased by Cross, her crush. Conchita, who knows about this crush, sabotages Lee's plan by deliberately getting her "out" during their fight.
The next semester is marked by two main plotlines. The first is Lee's relationship with her English teacher, Ms. Moray. Ms. Moray is very young and, like Lee, Midwestern. She does not fit in at Ault, and Lee feels a mixture of pity and antipathy towards her. The two get off to a difficult start, especially since Lee is hesitant to read her writing out loud in class. Ms. Moray takes it upon herself to inspire Lee and change her outlook, but Lee finds her teacher's behavior exhausting. The other students also dislike Ms. Moray, especially after she yells at three of them for performing a racist skit in class. When she is not in English class, Lee spends much of her time cutting hair. This begins by accident, when a somewhat oddball student named Tullis Haskell stumbles into Lee's dorm common room and asks for a haircut. She discovers that she is fairly good at haircuts, and begins to perform them free of charge for various students. Her roommate and best friend, Martha, warns her that this habit is unhealthy and allows others to take advantage of her. She intends to follow this advice but relents when Aspeth Montgomery, the grade's most popular girl, asks her for a haircut. Aspeth is accompanied to her haircut by Cross, and Lee finds that she likes Cross far less when he is in the company of the entitled Aspeth. At the chapter's end, Ms. Moray tells Lee that she will give her a good grade if Lee will agree to cut her hair. She does so, noticing the teacher's youth and obvious vulnerability. She reflects from her future perspective on how confused and ambitious Ms. Moray probably felt.
Events skip ahead a full year in Chapter Five, which opens with Lee preparing for parents' weekend. Her parents will be visiting Ault for the first time, and she is both excited and nervous. When they arrive, she feels by turns happy to see them and frustrated with their obvious nervousness at Ault. She is hyper-aware of their old car, their distinctly Midwestern friendliness, and their earnest desire to learn about Lee's school. She fights with her father when he insists on greeting a U.S. senator, whose daughter goes to school with Lee, but they overcome their bickering with jokes and teasing. Their final fight, though, escalates too far to be merely joked away. Lee invites two acquaintances, Rufina and Maria, to dinner in town with her family. The dinner goes smoothly, though Lee is overcome with anxiety throughout, but it ends badly when Rufina asks for a ride from Lee's parents to the more expensive hotel in town, where she hopes to meet a boy. Lee's father, uncomfortable with the idea of driving Rufina, refuses until Lee and Rufina collectively convince him. When Rufina has been dropped off and Lee's parents have driven her back to campus for the night, Lee's father tells her that he will be skipping the remainder of the weekend's events. He feels that Lee's boarding school experience has made her entitled and snobbish. Lee insults him in return, and he slaps her. The next day, Lee's mother calls tearfully to tell her that they are already driving back to Indiana. Though they joke about the disastrous weekend later, Lee continues to wonder about her father's feelings on that drive home.
The following term, Lee experiences a still greater shock: she is told that her former roommate Sin-Jun has attempted suicide. Sin-Jun is alive but hospitalized, and Lee is driven to the hospital to visit her friend. Sin-Jun's other visitor is her roommate Clara, who is sobbing uncontrollably by her bedside. Lee, overwhelmed by the atmosphere in the hospital room, wanders to the lobby. There she meets Dave Bardo, a member of Ault's kitchen staff, who happens to be at the hospital with his sister. Dave gives Lee a ride back to school. She develops a strong attraction to him during their drive, though she is also aware of the gulf between his status and her own at Ault. Back at school, she helps care for Sin-Jun by packing her an overnight bag for her move to the school infirmary. Lee learns that she is now the student primarily in charge of Sin-Jun, since Clara and Sin-Jun are feuding. Lee also encounters Dave again. Dave asks her out, and she agrees, though she is nervous about their date. She rides to the hospital with Sin-Jun's exhausted father to pick her up, and Sin-Jun seems grateful for Lee's help, but remains quiet and is not forthcoming about her emotions. Later, Lee goes to visit Sin-Jun in the infirmary and discovers her having sex with Clara. A flash into the forward lets readers know that Lee remains friends with Sin-Jun, who will one day live in Seattle with her girlfriend and work as a neurobiologist. Back at school, Lee learns that Sin-Jun will be taking the rest of the year off. Meanwhile, Dave finds Lee at a table in the dining hall and chats with her about the logistics of their date. He guesses from her awkwardness that she is unwilling to reveal their relationship to her friends and tablemates, and, insulted, he storms away. She wonders whether they might have enjoyed a fulfilling relationship if not for her discomfort.
Over the course of Chapter Seven, Lee deals with two vastly different problems on a similar timeline. Martha has been unexpectedly nominated for senior prefect and is running against more popular students, who are likely to win and feel entitled to do so. Lee, who is failing math, fears expulsion from Ault unless she passes a final exam. She has undergone tutoring with her kindly teacher Ms. Prosek, but, feeling awkward about her low performance, has left Ms. Prosek and is now tutored by a younger student named Aubrey. She spends her tutoring sessions trying to distract him from the subject matter and speak about more interesting topics, in spite of her panic. Meanwhile, Dede seeks out Lee to tell her, somewhat threateningly, that Martha is unlikely to win the prefect election against Dede's friend Aspeth. Lee's own feelings on the topic are growing complicated: she has begun to envy Martha, especially since Martha was nominated for the position by Lee's crush Cross. Still, she defends her friend, especially when Aspeth Montgomery herself tries to convince Lee to pressure Martha into dropping out of the race. The plotlines culminate on the same day. Martha wins the election (with Cross selected as the boys' prefect), and this is announced during morning roll call. Lee flees the scene to pick up her take-home exam, but is so intimidated by the questions that she lies in her room eating snacks instead of working. Martha discovers her there and furiously completes as much of the test as possible for Lee. That night, Martha cries, and Lee realizes that she is more upset about cheating than she is thrilled about winning the election.
The book's final chapter is primarily concerned with Lee and Cross's relationship. Lee wakes up one night to find Cross in her room. She lets him climb into her bed and the two kiss, though they stop short of having sex. However, he continues to visit her. Eventually, so as not to intrude on Martha, they begin meeting instead in a room used by a day student on the rare occasions that she sleeps at Ault. They have sex, and Lee looks forward to their meetings with an all-consuming excitement, but she has mixed feelings about their relationship. She wants to be Cross's girlfriend and hopes her peers will learn about what has happened between them, but also wants to appear undemanding, making Cross think that she is seeking a non-exclusive, secret relationship that is purely sexual. For instance, she casually tells Cross that she does not expect him to send her flowers, but hopes he will send her one in the school Valentine's Day exchange and is devastated when he does not. In the midst of this drama, Lee is asked to participate in an interview with a reporter who is writing about the state of prep schools. Feeling comfortable with the reporter, she spills her true feelings about Ault's exclusive atmosphere and about the longing for a more privileged lifestyle that propelled her to apply. As a result, both Ault students and her own family are angered after the article's publication, feeling that Lee has acted ungratefully. In the wake of these events, Lee goes to find Cross, who has stopped visiting her and seems to have acquired a new love interest. She intends to express her feelings of anger and abandonment, but finds only Cross's roommate, who treats her rudely and reveals to her a list of the girls in the grade that many Ault boys keep. He explains that the list categorizes the class's girls as "fish" or "cheese" based on how they smell and taste to boys who have sex with them. The roommate, Devin, complains that Cross is the "custodian" of the list but has not filled out Lee's information. Lee is furious and finds Lee another night, in the gym. She confronts Cross about the list and their relationship. Cross denies being the "custodian" of the list, but expresses frustration with Lee's noncommittal, confusing attitude towards him in general. He tells Lee that she is not as different from other Ault students as she has always seemed to believe, and that her loneliness has in some ways been self-induced. They part on bitter terms. On one of the final nights before graduation, Lee attends an event for the senior class. She bursts into tears there and is led away by Darden Pittard, a popular Ault student who is black and was also interviewed by the reporter who spoke to Lee. He kindly tells Lee that she was tricked into telling the reporter the truth because of her whiteness: being black, he says, he has long understood that rocking the boat is not a risk worth taking. Lee's senior year winds down with graduation and a series of "senior week" parties all over New England. The morning after one of these parties in Boston, Lee finds herself on a T platform. She gazes out at the range of people living lives completely disconnected from Ault and feels momentarily amazed.
Chapter Eight also gives some clues about Lee's future after Ault. We learn that she keeps in touch with Sin-Jun, Dede, and Martha, and although she rarely speaks to Martha as an adult, believes her to be the closest friend of her life. She loses touch with Cross, but is informed, via Martha, that he marries and carries golf clubs in his car trunk. Lee attends the University of Michigan, goes to graduate school, and rarely speaks about Ault, in large part because she finds discussing it so overwhelming and intense.