The Secret History is a first-person narrative recounted by Richard Papen, one of the main characters in the book. Richard, a 28-year-old man, narrates a story concerning his former college friends. He reveals at the beginning that he and his friends killed Bunny, and then goes on to tell the story of how this event happened. At 19 years of age, Papen leaves Plano, California to study at Hampden College in Vermont. Richard begins studying ancient Greek with an enigmatic professor named Julian Morrow, who limits the size of his class to a small and elite group of students. As a result, Richard becomes very close with the other students in the class: Bunny Corcoran, Henry Winter, Francis Abernathy, and Charles and Camilla Macaulay, who are fraternal twins. Bunny is much less intellectual and sophisticated than the other students, and also seems to have far less money than they do.
During the late fall and early winter, Richard notices strange occurrences, especially when the group spends weekends at a country house belonging to Francis. He also gets the sense that there is a tension between Bunny and other members of the group. Over the extended winter break, Richard stays in Vermont while the other students all travel home or abroad. In February, when the other students begin to return to campus, Richard learns from Henry that he, Francis, Charles, and Camilla spent much of the fall trying to replicate a bacchanal, a traditional Greek ritual involving entering a different state of consciousness. One night in November, they succeeded, but ended up killing a farmer during the ritual. Although they tried to cover up the murder, Bunny found out, and has been blackmailing the group ever since. As the weeks pass, Bunny cruelly taunts the other students, driving them to decide that they must kill Bunny. In April, Henry, Richard, Francis, Charles, and Camilla intercept Bunny during one of his regular walks, and push him over the edge of a ravine, hoping that the death will appear accidental.
Due to an unexpected snowfall, it takes a long time for Bunny's body to be discovered. Once the body is found, there is an extensive investigation, and both Charles and Henry are questioned by the FBI. The group of friends begins to fracture due to the tension of the investigation, and their guilt about what they have done. Richard realizes that Charles is an alcoholic, and that Charles is also obsessively jealous of his sister, with whom he appears to have an incestuous relationship. When Camilla moves out of the apartment she shared with Charles and begins a relationship with Henry, Charles becomes angry and aggressive. Shortly before the end of the semester, Julian receives a letter Bunny sent before his death, and realizes that his students most likely killed their classmate. Julian abruptly leaves the college, and is never seen again.
With their academic futures in jeopardy, the relationship between the friends crumbles even further. In a violent rage, Charles confronts Henry, planning to shoot him. He ends up shooting Richard by accident. Henry seizes the gun, and then shoots and kills himself in front of all the other friends. After the death, Charles, Camilla, and Francis all scatter, and only Richard returns to his studies the following year. He graduates from Hampden and goes on to pursue graduate studies back in California. After years of limited contact, Richard receives a suicide note from Francis and rushes to Boston to be with him. Francis has indeed tried to kill himself, but has not succeeded, and Camilla has also come to be with him. Camilla tells Richard that Charles has never fully recovered from his addiction, while she has largely given up her life to take care of their elderly aunt. Richard asks Camilla to marry him, but she declines, and they part ways. The novel ends with Richard having a vivid dream about Henry, signaling that he will never truly move on from the traumatic events he experienced.
