The Secret History begins with Richard Papen revealing that he and his friends have gotten away with killing someone named Bunny. The story he is about to tell promises to reveal how and why this happened.
Richard grows up in Plano, California, the son of working-class parents. After deciding that he cannot stomach the pre-med classes at his local community college, Richard decides to apply to Hampden College, a private liberal arts school in Vermont. Richard is accepted at Hampden, where he decides to study Greek under the tutelage of Julian Morrow. Julian is an enigmatic and charismatic professor with peculiar teaching methods. He insists that he acts as academic advisor to all of his students—of which there are only six, including Richard—and that the vast majority of their classes be with him.
After becoming Julian’s pupil, Richard gets to know his fellow Greek students: Henry, Bunny, Francis, and Charles and Camilla (who are twins). Often throughout Richard’s first semester, all the Greek students go to Francis’s country house on the weekends. Richard has fond memories of these weekends, even though he will later learn that things are not entirely as they seem. Primarily, Richard spends his energy on learning Greek and hiding his background from his new friends. In particular, Henry and Francis are quite wealthy, and Richard is embarrassed about his working-class upbringing.
During winter break, Richard lives for free in a warehouse while working at school. Unfortunately, he is ill-equipped to handle winter in Vermont, and he almost dies from the cold. Luckily, Henry comes back early from a trip to Italy and lets Richard live in his apartment until school starts. While living with Henry, Richard witnesses a number of odd exchanges between Henry, Bunny, and Francis. After some sleuthing, he eventually finds out that Henry has booked four plane tickets to South America, which depart right before the start of the semester. Additionally, he doesn’t see or hear from any of the other Greek students leading up to the start of the semester. As such, Richard eagerly awaits the start of classes so that he can figure out what is going on. However, when classes start, everything appears normal. All of the other Greek students show up on time for class and greet him excitedly, albeit with some rather unconvincing excuses.
Not long after classes begin, Henry decides to tell Richard the truth. He knows that Richard found out about the flight to South America and wants to explain what happened. As it turns out, Henry and the other Greek students spent most of the previous semester performing rituals and trying to induce Dionysian madness, which is a sort of pre-civilized euphoric state associated with the Greek god Dionysus. Because Bunny was not taking their attempts seriously, the other Greek students decided that he could no longer take part in their rituals. Then, once Bunny was out of the group, the Greek students succeeded in inducing Dionysian madness. However, in doing so, they accidentally killed a local man. They got away with the crime, but Bunny eventually learned what they did and is now blackmailing them for money (though in a rather casual, friendly way). Henry is worried that they will run out of money soon, which is why he and the other Greek students considered leaving for South America. He’s also worried that Bunny will tell somebody what he knows.
Not knowing what else to do, the Greek students decide to kill Bunny. They hide out in the woods where they know he likes to walk, and when he appears, they crowd around him and Henry pushes him into a ravine. After Bunny’s murder, it takes the authorities 10 days to find his body. During that time, Henry and Charles are questioned by the FBI, but ultimately Bunny’s death is ruled to be an accident. In the days following the recovery of Bunny’s body, the Greek students go to stay at Bunny’s parents’ house and attend his funeral.
In the weeks following Bunny’s funeral, relationships begin to dissolve between the Greek students. Charles begins drinking heavily and one night he crashes Henry’s car after the two of them get into a fight. Eventually it is revealed that Charles is jealous of Henry because Henry is in a secret relationship with his sister. Previously, Charles and Camilla were in an incestuous relationship with one another, but Camilla moved out of their shared apartment because Charles became abusive after Bunny’s death. In addition, Charles worries that Henry wants to kill him, since Henry seems to think Charles might go to the police.
Around the same time, Julian tells Richard and Francis that he’s received a previously lost letter that purports to be from Bunny. The letter talks about the man that the Greek students murdered and Bunny’s apparent fear that Henry wants to murder him. Julian dismisses the letter as fake, but Richard and Francis quickly realize that it’s genuine and try to get it away from Julian before he figures out the truth. However, they fail to do so, and Henry is forced to explain to Julian everything that has happened over the past several months. In response, Julian gives Henry the letter and then flees from Hampden, never to be seen there again.
After Julian’s departure, the situation between Henry and Charles continues to escalate. In an attempt to calm Charles down, Richard and Francis take him to the country house. However, while there, Charles overhears a phone conversation between Richard and Henry that makes him paranoid. In response, he flees the country house, and no one is able to find him. Desperate for help, Richard and Francis go to the inn that Camilla is staying at, where they find Camilla and Henry. Shortly after their arrival, Charles bursts in with a gun and threatens to shoot Henry. The gun is wrestled away from him, but not before he pulls the trigger, causing Richard to be shot in the stomach. The gunshot creates an uproar at the inn, and the Greek students worry that they will end up in jail after all. However, as the innkeeper opens the door, Henry uses the gun to shoot himself twice in the head. The Greek students then use Henry’s death to explain away the situation. They tell the authorities that Richard tried and failed to stop Henry from killing himself, which is how he sustained his gun wound.
After Henry’s death, Richard is the only one to return to Hampden the following semester where he eventually graduates with an English degree before returning to California for graduate school. While writing his dissertation, Richard receives a letter from Francis that essentially functions as a suicide note. Concerned, Richard flies to Boston, where he finds Francis recovering in a hospital from an attempted suicide. Camilla also shows up, and the three of them have a brief reunion. Camilla tells Richard and Francis that she no longer speaks to Charles, but she knows that he lives in Texas with a woman he met in rehab (though both of them continue to drink). Before leaving Boston, Richard asks Camilla to marry him, but she declines because she still loves Henry. The novel ends with Richard describing one of his recent dreams featuring Henry. He dreams that he and Henry are in a museum with an exhibit that morphs into various marvels of architecture. Henry tells Richard that he is not happy where he is but then says to Richard, “you’re not very happy where you are either,” before walking away down a “long, gleaming hall.”
