The Author's Note, preceding Chapter 1, explains that the author has traveled to India, restless and in need of inspiration for a story. At a coffeehouse in Pondicherry, an elderly man named Francis Adirubasamy strikes up a conversation with the author saying, I have a story that will make you believe in God. He refers the author to Piscine Molitor Patel who lives in Toronto, Canada. The novel then begins in Piscine's voice.

Piscine is an ardent teenager growing up in Pondicherry, an area of southern India that was once part of French India. The family, consisting of Piscine, his parents, and his playfully irritating older brother, Ravi, is happy. His life is rich with unique and wonderful educational opportunities. His father runs the Pondicherry Zoo where Piscine learns the psychology and husbandry of animals. (One such lesson in the workings of the natural world comes when Piscine's father explicitly demonstrates for Piscine and Ravi how a starving Bengal tiger reacts to a goat being introduced into its pen.) Piscine's mother reads widely and has an extensive assortment of books and literature which Piscine is encouraged to explore. In addition, Piscine's thirst for knowledge is nurtured by good schools and excellent teachers, in particular his atheist science teacher, Mr. Kumar, who inspired Piscine to study zoology.

Piscine is named after a famous swimming pool in France. A good friend of the family, Francis Adirubasamy, had been a champion competitive swimmer and touts the glory of the Piscine (pool) Molitor in Paris and thereby influences the parents' choice of the name. Schoolmates tease Piscine (pronounced Pea - seen) calling him pissing. In response to this verbal bullying, when Piscine enters the next level of school he rushes up to the blackboard during roll and announces his full name, underlining the first syllable, instructing all to know him as Pi. He proceeds to illustrate his new name with the mathematical explanation of the Greek letter pi, the letter that looks like a shack with a corrugated tin roof. The name catches on and Pi is thrilled.

Along with his search for knowledge, Pi is also in search of God. He grew up Hindu, but at age 14, he meets Jesus Christ via a Catholic priest named Father Martin. He asks to be baptized. Soon after, he meets another Mr. Kumar, this one a devoutly practicing Muslim, and converts to Islam as well. Pi happily practices all three religions simultaneously, even asks his father to buy him a prayer rug so he can face Mecca to pray. Once, upon a chance meeting at the zoo, the priest (Catholic), the pandit (Hindu), the imam (Muslim), and Pi's parents discover Pi's triple religious affiliation and argue that Pi must choose one. Pi responds, embarrassed, that he just wants to love God.

As the adult Pi narrates his story, he includes seemingly random, but informative discussions of religion, zoology, and Indian culture. During the interview process, the author also interjects his own observations about Pi, his home, and even his cooking.

Despite the abundance of wonder in Pi's India, there is political unrest. At 16, Pi does not fully understand the politics, but he knows that it is Mrs. Gandhi's actions that cause his father to decide to close the zoo and relocate to a better life in Canada. The zoo animals are sold, mostly to zoos in America, packed up, and loaded onto a freighter called the Tsimtsum, to travel to Winnipeg, Canada with the family. However, midway across the Pacific, the ship sinks.

Pi is the only survivor, in a lifeboat with a hyena and a zebra with a broken leg. He sees another survivor, Richard Parker, swimming frantically. Pi calls to him and throws him a lifebuoy. Full of panic and despair over losing his family, Pi encourages Richard Parker to swim to the lifeboat. Richard Parker finally makes it and jumps in to the boat. Pi comes to his senses and realizes that he has just invited Richard Parker, a 450 pound Bengal tiger into the lifeboat. Pi turned around, stepped over the zebra and threw [him]self overboard.

Now even more frightened of the black depths of the ocean and the triangular fins nearby, Pi wedges an oar under the tarpaulin at the bow of the boat and pulls himself out of the water. He decides that he might possibly survive if the tiger stays under the tarpaulin and he stays quiet and still on top. So he inches up the oar and reboards the boat.

A short distance away, Pi sees Orange Juice, a female orangutan, drifting toward the boat on a raft of netted bananas. When she nears, she climbs on board. What follows is a week of terror as Pi watches the gruesome food chain play out. The hyena eats the zebra, alive. Then after repeated screaming matches and mutual batting, the hyena finally eats the orangutan. Richard Parker eats the hyena.

The majority of the rest of the story is about Pi's 227 days at sea. He soon realizes that his only hope for survival is to tame Richard Parker. Oars and lifejackets are tied together to make a raft that will float, tethered, behind the lifeboat. This is Pi's safe zone. Drawing on his knowledge of animal behavior, Pi convinces Richard Parker that he is the alpha male. He uses the whistles from the life jackets as his tamer's whip and treats from the ocean as behavior rewards. He marks his territory, his half of the lifeboat, with urine and vomit. Though he is still in fear of the tiger, Pi keeps Richard Parker at bay by keeping him supplied with food and fresh water until he feels safe enough to spend time on the lifeboat, not just on the raft.

Over time, Pi develops a deepening bond with Richard Parker. A sort of zookeeper/animal relationship maintains the truce. But more than that, Richard Parker becomes Pi's reason for living. The formerly vegetarian Pi learns to kill and eat anything he can, and shares his catch with the tiger. He includes prayer in his daily routine and often marvels at the splendor of nature. However, as months drag on Pi's and the tiger's health deteriorate. They both lose their vision temporarily. Incredibly, while blind, Pi drifts into the lifeboat of another blind castaway. At first Pi thinks he is hallucinating about a conversation with the tiger, but then realizes it is indeed another man. The two men talk about food at length. Not knowing about Richard Parker, the other castaway boards Pi's boat with the intent of killing and eating Pi. Dramatically, the tiger's killer instinct saves Pi as well as provides Richard Parker with a meal. Pi is distraught over the other man's death and cries so hard that his tears actually help to clean out his eyes and partially restore his vision.

In cycles of hope and despair, it soon seems that the possibility of survival is lost. Barely alive, Pi and the tiger drift into a floating island that seems to be made of knotted masses of algae. Richard Parker climbs off of the boat onto the island. Pi samples the algae as food. The two stay on the island and regain their strength, returning to the boat at night. Pi discovers thousands of meerkats living on the island, as well as freshwater ponds. At night, the meerkats take to the trees. On attempting to stay in the trees one night with the meerkats, Pi discovers to his horror that the algae that makes up the island secretes acid at night that will digest anything left on its surface. Pi finds human teeth within the algae and concludes that it is a carnivorous island that may have even digested a previous castaway who died there. Alarmed, Pi returns to life adrift on the boat, which has become a butchery, a circus ring, and a place of prayer.

When they reach land (Mexico), Pi is exhausted and weak. Richard Parker simply gets out of the lifeboat and disappears into the jungle. Officials representing the shipping company of the Tsimtsum come to Mexico to question the recovering Pi. They find Pi's story of his 227 days at sea too implausible to believe. Pi counters their incredulity with facts and reason, but the investigators are still doubtful. So Pi tells them a completely different story, a story that includes in the lifeboat Pi's mother, a sailor with a broken leg, and a French cook.

The second story has murder and cannibalism, but no animals and no floating island. One investigator notes the parallels between the people and the animals of the two stories, but the other dismisses them. They seem satisfied. Pi says to the men, In both stories the ship sinks, my entire family dies, and I suffer, to illustrate that there is no factual difference in the outcomes of the two stories. He then asks the men which story they prefer. They admit to preferring the story with the animals, the better story. And so it goes with God, is Pi's response. The better story is what ends up in the men's report.