During the year 1866, ships of various nationalities sight a mysterious sea monster, which might be a gigantic narwhal. The U.S. government assembles an expedition in New York City to find and destroy the monster. Professor Pierre Aronnax, a French marine biologist and the story's narrator, is in town at the time and receives a last-minute invitation to join the expedition. Canadian whaler and master harpooner Ned Land and Aronnax's faithful manservant Conseil are also among the participants.
The expedition leaves Brooklyn aboard the United States Navy frigate Abraham Lincoln, then travels south around Cape Horn into the Pacific Ocean. After a five-month search ending off Japan, the frigate locates and attacks the monster, which damages the ship's rudder. Aronnax and Land are hurled into the sea, and Conseil jumps into the water after them. They survive by climbing onto the "monster", which, they are startled to find, is a futuristic submarine. They wait on the deck of the vessel until morning, when they are captured and introduced to the submarine's mysterious constructor and commander, Captain Nemo.
The rest of the novel describes the protagonists' adventures aboard the Nautilus, which was built in secrecy and now roams the seas beyond the reach of land-based governments. In self-imposed exile, Captain Nemo seems to have a dual motivation — a quest for scientific knowledge and a desire to escape terrestrial civilization. Nemo explains that his submarine is electrically powered and can conduct advanced marine research; he also tells his new passengers that his secret existence means he cannot let them leave — they must remain on board permanently.
They visit many oceanic regions, some factual and others fictitious. The travelers view coral formations, sunken vessels from the Battle of Vigo Bay, the Antarctic ice barrier, the transatlantic telegraph cable, and the legendary underwater realm of Atlantis. They even travel to the South Pole and are trapped in an upheaval of an iceberg on the way back, caught in a narrow gallery of ice from which they are forced to dig themselves out. The passengers also put on diving suits, hunt sharks and other marine fauna with air guns in the underwater forests of Crespo Island, and attend an undersea funeral for a crew member who died during a mysterious collision experienced by the Nautilus. When the submarine returns to the Atlantic Ocean, a school of giant squid ("devilfish") attacks the vessel and kills another crewman.
The novel's later pages suggest that Captain Nemo went into undersea exile after his homeland was conquered and his family slaughtered by a powerful imperialist nation. Following the episode of the devilfish, Nemo largely avoids Aronnax, who begins to side with Ned Land. Ultimately, the Nautilus is attacked by a warship from the mysterious nation that has caused Nemo such suffering. Carrying out his quest for revenge, Nemo — whom Aronnax dubs an "archangel of hatred" — rams the ship below her waterline and sends her to the bottom, much to the professor's horror. Afterward, Nemo kneels before a portrait of his deceased wife and children, then sinks into a deep depression.
Circumstances aboard the submarine change drastically: watches are no longer kept, and the vessel wanders about aimlessly. Ned becomes so reclusive that Conseil fears for the harpooner's life. One morning, however, Ned announces that they are in sight of land and have a chance to escape. Professor Aronnax is more than ready to leave Captain Nemo, who now horrifies him, yet he is still drawn to the man. Fearing that Nemo's very presence could weaken his resolve, he avoids contact with the captain. Before their departure, however, the professor eavesdrops on Nemo and overhears him calling out in anguish, "O almighty God! Enough! Enough!". Aronnax immediately joins his companions as they carry out their escape plans, but as they board the submarine's skiff they realize that the Nautilus has seemingly blundered into the ocean's deadliest whirlpool, the Moskenstraumen (more commonly known as the "Maelstrom"). Nevertheless, they manage to escape and find refuge on an island off the coast of Norway. The submarine's ultimate fate remained unknown until the events of The Mysterious Island.
