At the opening of the book, the narrator, an everyman named John (a.k.a. Jonah), describes a time when he was planning to write a book about what important Americans did on the day Hiroshima was bombed. While researching this topic, John becomes involved with the children of Felix Hoenikker, a fictional Nobel laureate physicist who helped develop the atomic bomb. John travels to Ilium, New York, to interview the Hoenikker children and others for his book. In Ilium John meets, among others, Dr. Asa Breed, who was the supervisor “on paper” of Felix Hoenikker. As the novel progresses, John learns of a substance called ice-nine, created by the late Hoenikker and now secretly in the possession of his children. Ice-nine is an alternative structure of water that is solid at room temperature. When a crystal of ice-nine contacts liquid water, it becomes a seed crystal that makes the molecules of liquid water arrange themselves into the solid form, ice-nine.
John and the Hoenikker children eventually end up on the fictional Caribbean island of San Lorenzo, one of the poorest countries on Earth, where the people speak a barely comprehensible creole of English (for example “twinkle, twinkle, little star” is rendered “Tsvent-kiul, tsvent-kiul, lett-pool store”). It is ruled by the fictional dictator, “Papa” Monzano, who threatens all opposition with impalement on a giant hook.
San Lorenzo has an unusual culture and history, which John learns about while studying a guidebook lent to him by the newly-appointed US ambassador to the country. He learns about an influential religious movement in San Lorenzo, called Bokononism, a strange, postmodern faith that combines irreverent, nihilistic, and cynical observations about life and God’s will with odd, but peaceful rituals (for instance, the supreme act of worship is an intimate act consisting of prolonged physical contact between the bare soles of the feet of two persons, supposed to result in peace and joy between the two communicants). Though everyone on the island seems to know much about Bokononism and its founder, Bokonon, the present government calls itself Christian and those caught practising Bokononism are punished with death by the giant “hook.”
As the story progresses, it becomes clear that San Lorenzon society is more bizarre and cryptic than originally revealed. In observing the interconnected lives of some of the island’s most influential residents, John learns that Bokonon himself was at one point a de facto ruler of the island, along with a US Marine deserter. The two men created Bokononism as part of a utopian project to control the population. The ban was an attempt to give the religion a sense of forbidden glamour, and it is found that almost all of the residents of San Lorenzo, including the dictator, practice the faith, and executions are rare.
When John and the other travelers arrive on the island, they are greeted by President “Papa” Monzano and around five-thousand San Lorenzans. It becomes clear that “Papa” Monzano is extremely ill, and he intends to name Franklin Hoenikker his successor. Franklin, uncomfortable with this arrangement, abruptly hands the presidency to John, who grudgingly accepts.
The dictator later uses ice-nine to commit suicide rather than succumb to his inoperable cancer. Consistent with the properties of ice-nine, the dictator’s corpse instantly turns into solid ice at room temperature.
During John’s inauguration festivities, in which the American ambassador to San Lorenzo was going to speak, San Lorenzo’s small air force was supposed to present a brief air show. One of the airplanes crashes into the dictator’s seaside palace and causes his still-frozen body to tumble into the ocean, and all the water in the world’s seas, rivers, and groundwater turns into ice-nine, killing almost all life in a few days.
John manages to escape with his wife, a native San Lorenzan named Mona. They later discover a mass grave where all the surviving San Lorenzans had killed themselves with ice-nine, on the facetious advice of Bokonon. Displaying a mix of grief and resigned amusement, Mona kills herself as well. John takes refuge with a few other survivors (an American couple he had met on the plane to San Lorenzo and Felix Hoenikker’s two sons), and lives in a cave for several months, during which time he writes a memoir revealed to be the novel itself. The book ends by his meeting a weary Bokonon, who is contemplating what the last words of The Books of Bokonon should be. John receives inspiration from these words and the reader realizes he is planning to place his own book—a “history of human stupidity”—on Mt. McCabe (the highest point on the island) as a “magnificent symbol” and then die.