In 1866 the world's shipping is alarmed by sightings of an enormous, fast, faintly glowing object that no whale could match. Pierre Aronnax, a Paris museum professor of natural history, is invited to join an American expedition to hunt it down. He sails with his devoted servant Conseil, and aboard the frigate meets Ned Land, a Canadian harpooner of great skill and little patience. After a long fruitless chase the creature strikes back, and the three are thrown into the sea.
They are pulled onto the surface of the thing itself, which proves to be not an animal but a submarine vessel of metal, the Nautilus. Its commander, who calls himself Captain Nemo, tells them plainly that they have surprised a secret no one may carry back. He will treat them well, but they will never leave. They are, he says, his prisoners of war, kept not out of cruelty but to protect the secret of his whole existence.
Nemo turns out to be a man of immense learning and wealth who has cut every tie to land. The sea, he says, supplies all his wants, and beneath thirty feet of water the unjust laws and despots of the surface lose all power over him. He shows Aronnax a library, a museum of art and natural treasures, and a craft run entirely by electricity drawn from the ocean. To the professor it is a captivity filled with wonders he could never have reached alone.
The Nautilus crosses the great oceans, and Aronnax records marvel after marvel: a forest walk along the seabed, a coral cemetery where the crew bury their dead, a pearl of fabulous size, the wreck-strewn floor of vanished battles, and at last the unclaimed ice of the South Pole, where Nemo plants a black flag. Danger travels with the beauty, from sharks and an ice entombment that nearly suffocates them to a battle with giant squid in which a sailor is lost.
Slowly the mystery behind Nemo darkens. He weeps over a sunken hulk, names his vessel after the Avenger, and finally rams and sinks a warship of a nation he will not name, crying that through its people he lost country, wife, and children. Aronnax, unable to share or excuse such retaliation, resolves to flee. As the Nautilus is drawn toward a deadly Norwegian maelstrom, the three escape in its small boat, and the professor wakes ashore, never to learn the captain's name or fate.