Paul Murray's Skippy Dies opens with its titular character collapsing and dying during a doughnut-eating contest at Ed's Doughnut House, writing 'tell Lori' in jelly filling as his final act. The novel then moves backward chronologically to explore the events leading to this tragedy at Seabrook College, one of Ireland's most prestigious Catholic boarding schools.

Seabrook College represents traditional Irish institutional authority in decline. Historically run by the Holy Paraclete Fathers, the school now operates under its first lay principal, Greg Costigan, known as 'the Automator,' who temporarily fills in for the ailing Father Desmond Furlong. The Automator embodies bureaucratic ambition and institutional self-preservation, planning to transform the school's 140th anniversary concert into a memorial for the still-living Father Furlong to advance his own career prospects.

Skippy lives in the school dormitory with his roommate Ruprecht, a brilliant boy obsessed with theoretical physics who has told everyone his parents died in an Amazonian kayaking accident. Their friend group includes Mario, Geoff, and Dennis. Skippy struggles academically and socially until he begins taking pills that dramatically improve his swimming performance, transforming him from outcast to athletic star overnight. However, this pharmaceutical enhancement masks deeper psychological struggles related to his mother's terminal cancer, which his family refuses to acknowledge through an elaborate game of denial.

The adult authority figures consistently fail the students in their care. Howard Fallon, a history teacher nicknamed 'Howard the Coward,' cannot engage his students and becomes obsessed with Aurelie McIntyre, a beautiful substitute geography teacher who usually works as an investment banker. Howard's romantic fantasies lead him to confess his feelings to Halley, his long-term girlfriend. His confession destroys their relationship for the prospect of an affair that proves meaningless to Aurelie, who becomes engaged to her longtime boyfriend.

Father Jerome Green represents the toxic intersection of religious authority and psychological damage. One of Seabrook's oldest and most terrifying priests, he humiliates Skippy in French class by publicly interrogating him about his virginity, causing the already fragile boy to vomit. Father Green's harsh treatment of students stems from his own guilt over sexually abusing children during his missionary work in Africa, making his recognition of Skippy's purity and gentleness particularly disturbing.

The novel's central romantic plot involves Skippy's infatuation with Lori, a St. Brigid's girl he spots from his dormitory window using Ruprecht's telescope. At the Hallo'een Hop, a mixer between the two schools, Skippy courageously approaches Lori despite knowing she has connections to Carl, a violent student everyone fears. Carl represents toxic masculinity and unchecked rage. He sells stolen prescription drugs with his accomplice Barry while harboring misogynistic fantasies. His obsession with Lori leads him to contaminate the dance's punch with date-rape drugs when he's denied entry.

While Howard abandons his chaperoning duties to have sex with Aurelie in her classroom, Skippy and Lori bond over shared drug use and genuine conversation. She reveals her dreams of becoming a singer while he admits his hatred of swimming. Their connection culminates in a successful date at her house, where her parents warmly welcome Skippy. Her father tells him about Coach Tom Roche's tragic bungee jumping accident years earlier that ended his rugby career.

The novel's darkest revelation emerges through fragmented, dream-like sequences suggesting that Coach Roche sexually assaulted Skippy during a previous swim meet. After Skippy's strong performance, he went to Roche's hotel room complaining of leg pain. Roche provided alcohol and sedatives before molesting the unconscious boy, creating trauma that Skippy cannot fully process or articulate.

Carl's rage intensifies when Lori cuts off contact with him. He manipulates her friend Janine sexually while fantasizing about revenge against Skippy. When Carl finally convinces Lori to meet him, he secretly videotapes her performing oral sex and distributes the footage throughout Seabrook. Carl's violence escalates to lighting Skippy's locker on fire, prompting Skippy to challenge him to a fight. During the confrontation, Carl's self-harm scars are revealed to the assembled crowd, adding complexity to his character by showing his own victimization.

Meanwhile, Ruprecht attempts to cope with the institutional dysfunction through scientific experimentation, creating a teleportation machine based on M-Theory. When the device appears to make an Optimus Prime figurine disappear, the boys interpret this as hope for escaping from their circumstances. They are planning on breaking into St. Brigid's to harness the power of ancient Irish mounds.

The mounting pressures—his mother's hidden illness, the academic threats of expulsion, the sexual assault trauma, and the pharmaceutical dependency—ultimately overwhelm Skippy. After emptying his pill bottle, he challenges Ruprecht to the doughnut-eating contest that opens the novel, deliberately overdosing in what becomes a suicide that rocks both schools.

The aftermath exposes institutional corruption at its worst. The Automator discovers Coach Roche's confession of sexual assault. He chooses to transfer the coach quietly rather than involve police. Additionally, he forces all attendees at a meeting to sign non-disclosure agreements to protect the school's reputation. This cover-up prevents even Skippy's parents from learning the truth about their son's death.

The novel concludes with the 140th anniversary concert disrupted by Ruprecht's desperate attempt to contact Skippy's ghost through modified musical frequencies, Carl's drug-induced arson that destroys the oldest part of Seabrook and kills Father Green, and The Automator's promotion to full principal. The institutional machinery continues operating despite the human devastation it has caused, suggesting that systemic dysfunction will persist unless fundamental changes occur in how societies protect their most vulnerable members.