The Secret History is the story of Richard Papen, one of six close friends studying the Classics at a fictional Vermont university. The novel begins with an older Richard discussing a murder that took place within the group and the destruction it wrought on he and his friends. The novel then proceeds to explore the motivations behind the murder and the effects it had on his life and the lives of its friends after their college years.
As the story opens, Richard leaves the (fictitious) small town of Plano, California, where he is generally unhappy, for Hampden College in Vermont. His disdain for his background establishes a contrast—aestheticism and literary beauty, as opposed to harsh reality—that continues throughout the novel. He misleads others about his background, replacing his mediocre working-class childhood with a fabricated, glamorous one of boarding schools, wealth, failed actors, and parents who own an oil well.
In Vermont, Richard tries to continue his study of Ancient Greek, only to be denied admittance to the course, as Classics professor Julian Morrow limits his enrollment to a tiny hand-picked coterie. Richard becomes obsessed with the group, observing them around campus and noting what he considers a cold attitude toward the world around them and an obsession with studies that he admires. Eventually, he manages to ingratiate himself with the group by helping to solve a Greek grammar problem. Soon after, armed with advice from the group on how to impress Morrow, Richard meets with him and is finally admitted to the Classics tutorial.
The group includes fraternal twins Charles and Camilla Macaulay, who are charming but secretive, as well as Francis Abernathy, whose secluded country home becomes a sanctuary for the group. (Francis reappears, in a sentence or two, in Tartt's later novel, The Goldfinch .) Two students become the central focus: linguistic genius Henry Winter, an intellectual with a passion for the Pali canon, Homer, and Plato; and back-slapping Bunny Corcoran, a bigoted jokester more comfortable reading Sax Rohmer's Fu Manchu novels.
The pair's friendship, which Richard finds odd, becomes more mystifying when Bunny announces that he and Henry will spend winter break together in Rome, Italy—although Henry appears to barely tolerate Bunny, and Bunny cannot afford such a lavish holiday himself. In fact, Henry is footing the bill for the trip. To avoid revealing his fabricated past, Richard takes a low-paying job on campus and spends winter break, the coldest in a generation, in an unheated warehouse. He nearly dies from hypothermia and pneumonia, but is rescued and taken to the hospital by Henry, who has returned early from Italy.
After winter break, Richard sees the relationship between the others and Bunny becoming even more strained. Ultimately, he learns the truth from Henry and Francis: during a Bacchanal (from which both Richard and Bunny were excluded), Henry inadvertently killed a local farmer who lived near Francis's country estate. Bunny, suspicious for some time, uncovered the truth during the trip to Italy by reading Henry's diary, and has been blackmailing the group since. The group, led by Henry, now view Bunny as a danger, and Bunny's penchant for playing on his friends' fears and insecurities does little to assuage their concern.
No longer able to meet Bunny's demands, and fearing that he will report them, the group resolves to kill Bunny. Henry forms several plots, one of which is finally put into motion after a drunken Bunny tells Richard of the killing. The group confronts Bunny while he is hiking, and Henry pushes him into a ravine to his death.
The rest of the novel follows the group's collapse, the psychological strains of remorse borne by the members, and their efforts to maintain secrecy as investigators and other students inquire into Bunny's disappearance. (The other students include loquacious drug user Judy Poovey, a reader of "those paranoia books by Philip K. Dick".) They attempt to act natural, joining the search parties combing over the campus looking for Bunny.
Charles develops a drinking problem and becomes increasingly abusive towards his sister Camilla. Francis confirms to Richard that the twins are having sexual relations. Francis himself begins to suffer panic attacks. Morrow discovers a pleading letter sent to him by Bunny, imploring him to help: "You're the only one who can." He never reports the crime, instead leaving the faculty. This action creates consequences for the main characters (though mainly just Richard, the only one without an inheritance at his disposal). Left without a teacher, they have little options for the coming academic year and will be unable to complete their majors, forced to change up their plans, though this is hardly the most troublesome thing on their minds.
As the group splinters, the members must deal with things in isolation. Henry begins living and sleeping with Camilla, which drives Charles further into alcoholism. Henry, deeply upset by Morrow's departure, sees it as an act of cowardice and hypocrisy. When Charles is arrested in a drunk driving incident with Henry's car, Henry fears Charles will let something slip to the police. The climax comes when Charles, jealous of Henry and now a full-blown alcoholic, barges into Camilla and Henry's hotel room and tries to kill Henry with Francis' Beretta. In the struggle, Henry gets hold of the gun; the others pile on him, and Charles ends up shooting Richard in the abdomen. The innkeeper, hearing the commotion and gunshot, forces his way into the room. Meanwhile, Henry kisses Camilla farewell and shoots himself fatally. Apparently, Henry, wishing to uphold the principles he feels Morrow has betrayed, covers for Charles, his suicide leading the police to conclude that Henry shot Richard.
With Henry's death, the group disintegrates. Francis attempts suicide and, though homosexual, is forced by his rich grandfather to marry a woman; Camilla, taking care of her grandmother, becomes increasingly isolated; Charles runs away from rehab with a married woman; and Richard, after recovering from his wounds, becomes a lonely academic with an unrequited love for Camilla. He sees Henry's death as having cut the cord that bound them, setting them all adrift. The book ends with Richard recounting a strange dream where he meets Henry in a tall atrium, unable to say all he feels about what has happened. Finally, he settles on asking, "Are you happy here?" Henry replies, "Not particularly. But you're not very happy where you are, either," and walks away.