Twenty Thousand Leagues Under the Sea begins with a mystery. For over a year, ocean-going vessels have reported running into a floating island or a submerged naval wreck, or being rammed by a giant whale. Pierre Aronnax, assistant professor at the Museum of Natural History in Paris, develops a theory to explain these confusing sightings; he believes that a huge narwhal is bedeviling these ships. After the Scotia, a Cunard Lines passenger ship, again encounters this "creature," the United States equips a speedy frigate, the Abraham Lincoln, to hunt and kill the dangerous beast. Because of his theory, Aronnax is invited to join the expedition along with Conseil, his servant. Ned Land, a famous Canadian harpooner, is brought along for his hunting skills.

After a long, unfruitful search, the Abraham Lincoln finally collides with the beast off the coast of Japan. Aronnax, Conseil, and Land are thrown overboard and grab hold of the monster's back to keep from drowning, only to discover that its skin is made of steel. The "creature" is actually a submarine.

The three are brought aboard the submarine, called the Nautilus, where they meet the mysterious Captain Nemo.

Their status on the ship seems ambiguous. Are they guests, as Nemo insists, or prisoners, as Ned Land begins to suspect? Nemo introduces them to the wonders of the underwater world. He shows them the lost continent of Atlantis and the wrecks he has plundered of gold. He takes them through a secret underwater passage from the Mediterranean to the Red Sea, a Suez passage where none existed in 1870.

Aronnax is fascinated by these underwater discoveries, but Ned Land becomes more impatient for his freedom.

When Nemo guides the Nautilus to the South Pole, the ship becomes entrapped in an ice pack. The Nautilus escapes from the ice, only to be attacked by a giant squid that nearly sinks the vessel.

Eventually, Aronnax's fascination with Nemo declines, as the Captain attacks passing ships, apparently for revenge or for greed. The Nautilus heads into northern waters, and the three captives plot their escape from Nemo's clutches, even as the ship blunders into a giant whirlpool.