Part I of the novel, consisting of twenty-three chapters, begins in the summer of 1866 when something enormous and mysterious is sighted at various locations on the ocean. This “sea monster” is treated as a tall tale at first, but when shipwrecks start to occur, Admiral Farragut of the U.S. Navy is sent on a mission to find the monster. He enlists the help of ocean expert Professor Pierre Aronnax of the Museum of Natural History in Paris, along with Aronnax’s servant, Conseil. Farragut also enlists a master harpooner from Canada named Ned Land who has unparalleled eyesight and a quick hand. The Abraham Lincoln sets off from New York City, and after searching the Atlantic, the frigate rounds Cape Horn and heads for the Pacific. There they find the monster, a man-made submarine that sprays enormous waterspouts at the frigate, damaging its rudder and knocking Aronnax, Conseil, and Land into the ocean.

The three men are taken captive aboard the Nautilus, the invention of Captain Nemo, who commands a devoted crew of men who live completely apart from society, even speaking their own invented language. The prisoners are well fed and soon realize the sophistication of their surroundings. Nemo tells them they are free on the ship, but they are not free to leave. If they don’t agree to the situation, Nemo will drown them. The vessel has an abundant library of books, art, and specimens, enticing to Aronnax. The crew prepares elaborate meals from sea products, and the whole enterprise is powered by electricity produced from sea minerals. The vessel must surface to take on air, but other than that, it is entirely self-sufficient.

Aronnax is astounded by the sea life that he can observe from inside the Nautilus and even more impressed with the intimacy of their walks on the sea floor wearing suits and helmets with individual lanterns. Nemo invites the captives on a deep-sea hunting expedition in a submarine forest. They use electric guns to kill prey. The captives spend a few days on land when the Nautilus runs aground near Australia and they must wait for high tide to set the Nautilus free. On the island, Aronnax, Conseil, and Land hunt real meat and encounter natives who chase them away. When the island natives try to get into the submarine, they are shocked by electric cables. As the Nautilus speeds to the Indian Ocean, Nemo orders Aronnax, Conseil, and Land to their quarters, where they sleep deeply after eating drugged food. The next morning, Nemo calls Aronnax to care for a wounded crew member, but the man dies. At the end of Part I, the captives attend the man’s burial in a breathtakingly beautiful underwater cemetery.

Part II also takes place in twenty-three chapters, starting up two years later than Part I, in January 1868. This part of the novel begins with Nemo inviting the captives on a pearl expedition near Ceylon, where he shows them an enormous pearl that he chooses not to harvest. During this expedition, Nemo is threatened by a shark, but Land saves him by harpooning it. They enter the Red Sea and discover that Nemo has found a subterranean passage, the Arabian Tunnel, that takes them to the Mediterranean Sea. One night, a diver appears outside the window of the Nautilus, and Aronnax witnesses Nemo handing over a chest of gold ingots to the diver. The vessel later passes through boiling waters caused by an underground volcano. Nemo maintains a high speed and feels cramped between the two continents. They pass through the Straits of Gibraltar and head to Virgo Bay, where Nemo retrieves treasure from a 1702 shipwreck. They go on another underwater excursion to see the lost city of Atlantis and spend time inside an extinct volcano while the crew extracts coal that will help power the Nautilus. They encounter some whales that Nemo forbids Land to hunt, but they purposely hit other whales, called “cachalots,” that threaten the other whales.

The Nautilus continues southward toward Antarctica, and Aronnax is astounded by the beauty of the icy world. When they are trapped by an iceberg, Nemo decides that they will dive under it even though they risk running out of air. His plan works. They determine that they are at the South Pole and prove that the pole is a land mass. Nemo plants a flag, claiming the Pole for his own as he is the first man to step on the land. Later, when the Nautilus is again trapped by a toppled iceberg, the situation turns dire. The men are running out of air. The men all work together and take turns digging at the ice walls with axes. On board the Nautilus, they grow dizzy and faint with lack of oxygen. At the last minute, the Nautilus breaks through the ice, and fresh air rushes in. During this ordeal, Conseil and Land save Aronnax’s life by sharing their last portion of air with him. The vessel moves northward to Cape Horn and speeds to the Caribbean, arriving by April 20. There, they encounter a group of giant squid who attack the vessel and kill one of the crew members before they can drive the creatures back into the sea.

After these challenges, Nemo grows sullen, silent, and absent. The Nautilus moves northward up the coast, but the weather is too rough for Aronnax, Conseil, and Land to attempt an escape. Nemo shows Aronnax a manuscript of his life history that he will shut into a waterproof case to be tossed into the sea by the last survivor of the Nautilus. A hurricane pushes the vessel farther out to sea, where they spot the failed transatlantic telegraph cable. Nemo tells the story of a sunken ship named the Avenger that sank with its crew exactly seventy-four years before. They spot an approaching warship. Nemo orders the captives below after the warship shoots at them. Nemo shouts his intention to take revenge. The Nautilus rams the ship, causing it to sink with all its crew. The scene ends with Nemo in front of the portrait of his wife and children, sobbing. Two weeks pass during which Aronnax does not see Nemo at all. The captives plan to escape one night near Norway’s coast. Just as they are about to escape, they see a maelstrom, a whirling storm that overtakes the vessel. Aronnax’s head strikes the hull, and he loses consciousness. When he wakes, he is with Conseil and Land on an island. They do not know what has happened to Nemo and the Nautilus.