The second part of the novel begins with Pi's family aboard the Tsimtsum, a Japanese freighter that is transporting animals from their zoo to North America. A few days out of port from Manila, the ship encounters a storm and sinks. Pi manages to escape in a small lifeboat, only to learn that the boat also holds a spotted hyena, an injured Grant's zebra, and an orangutan. Much to the boy's distress, the hyena kills the zebra and then the orangutan. At this point, Pi learns that a tiger has been hiding under the boat's tarpaulin: it's Richard Parker, who had boarded the lifeboat with ambivalent assistance from Pi himself some time before the hyena attack. Suddenly emerging from his hideaway, Richard Parker kills and eats the hyena.
Frightened, Pi constructs a small raft out of rescue flotation devices, tethers it to the stern of the boat and makes it his place of retirement. He begins conditioning Richard Parker to take a submissive role by using food as a positive reinforcer, and seasickness as a punishment mechanism, while using a whistle for signals. Soon, Pi asserts himself as the alpha animal, and is eventually able to share the boat with his feline companion, admitting in the end that Richard Parker is the one who helped him survive his ordeal.
Pi recounts various events while adrift in the Pacific Ocean. At his lowest point, exposure renders him blind and unable to catch fish. In a state of delirium, he talks with a marine "echo", which he initially identifies as Richard Parker having gained the ability to speak, but it turns out to be another blind castaway, a Frenchman, who tries to come aboard the lifeboat, but is eventually killed by Richard Parker.
Some time later, Pi's boat comes ashore on a floating island network of algae and inhabited by hundreds of thousands of meerkats. Soon, Pi and Richard Parker regain strength, but the boy's discovery of the carnivorous nature of the island's plant life forces him to return to the ocean.
Two hundred and twenty-seven days after the ship's sinking, the lifeboat washes onto a beach in Mexico, afterwhich Richard Parker disappears into the nearby jungle without looking back, leaving Pi heartbroken at the abrupt farewell.