Beginning in the year 1866, coastal communities around the world buzz with rumors of a sea monster. Sailors report seeing a large, fast-moving creature accompanied by a strange glow. Several ships, attempting to approach the creature, have been seriously damaged.
In 1867, renowned French naturalist professor Aronnax, who had been studying in America, publishes his theory on the monster. It could be an enormous narwhal, the horn of which could have caused the reported damage to the ships. Many people agree with his theory.
Just as Aronnax and his servant, Conseil, are preparing to leave New York to return to their home in France, Aronnax is invited to join the American vessel the Abraham Lincoln, whose crew plans to hunt down the narwhal. Aronnax, enticed by the thought of discovering the creature, cannot refuse. He and Conseil sail with the Abraham Lincoln to the Pacific Ocean, where the creature was last sighted. There, Aronnax befriends Ned Land, a Canadian harpooner.
After eight months, Ned Land spots the creature in Japanese waters. The Abraham Lincoln gives chase, but it can’t catch up to the creature. Ned’s harpoon hits the creature. The monster collides with the ship. Aronnax and Conseil are thrown overboard on impact. After a long night of swimming, the two find Ned Land, who was also thrown overboard. Ned had taken refuge from the waters on the creature—which turns out not to be a narwhal, but an iron ship. Eventually crewmembers find the three castaways on their ship and bring them inside. The crew speaks an odd language, and Aronnax and his friends are left in a dark room without explanations for some time.
After a few days, the three meet Captain Nemo, a reclusive genius, who built the submarine, The Nautilus, in order to live and explore, unbothered by human society. His crew is made up of others who also have chosen a life of seclusion. Nemo declares Aronnax and his friends are prisoners of war, since Ned tried to harpoon his ship. He won’t allow them to return to the world above, for fear of being discovered. However, he will allow them to live on The Nautilus, in comfort.
Ned Land is furious, but Aronnax and Conseil are fascinated. Nemo has a high respect for Aronnax. The two have many long conversations about how The Nautilus works.
Over several months, Aronnax learns more about the world’s oceans than he was ever been able to on land. The Nautilus is equipped with powerful electric lights — the glowing that sailors reported — and large windows that allow a perfect view outside. Nemo has constructed diving suits that allow people to take walks along the ocean floor. He uses these suits to make his living: He and his crew find sunken ships and take whatever treasures remain. He also has a collection of ocean finds, from shells to pearls, onboard that Aronnax declares more valuable than that of any museum in France. Nemo allows Aronnax to accompany him on many of these trips — including one to visit the lost city of Atlantis.
One day, Nemo demands that the prisoners return to the dark room where he first kept them. Aronnax suspects the ship is under attack. Nemo drugs their food so that they fall asleep after dinner. When the three wake up, all seems normal, except for one crewmember. Nemo asks Aronnax to inspect him. The crewmember suffers from a mortal head wound. Aronnax can do nothing for him, and he dies in the night. The next day, Nemo and the crew bury the man in a coral reef.
Ned Land longs to return home. He and Counseil, who share a room, plot to escape. Aronnax half-heartedly helps — he misses France, but he’s reluctant to leave The Nautilus, the only place he can truly study in peace. In spite of Ned’s hopes, Nemo never brings the ship close enough to land to allow them to escape. Ned Land grows more and more despondent.
Nemo charts a course to the South Pole, a region no man has seen. The Nautilus weaves its way through fields of ice, eventually having to go beneath icebergs in order to reach the very end of the world. The ship finally arrives at the South Pole. Because this is land no other man has trod, Nemo exits his ship to explore it, eventually claiming it as his own. As they continue their ocean journey, a falling piece of ice traps The Nautilus inside a submerged cavern in an iceberg. Unable to replenish their supply of air, the crew spends five days trying to escape, slowly suffocating. Toward the end, Aronnax nearly dies, but Conseil and Ned Land have saved some air from their diving suits, which they give to him. Finally, The Nautilus reaches the surface. Aronnax thanks his companions for saving his life.
A few days after, a group of giant squid descends upon the ship. A bloody battle ensues as the crew attempts to defend themselves. Although Nemo and his men eventually defeat the monsters, one of the crewmembers is carried away into the depths of the sea. Nemo is crushed, growing even more reclusive in his sorrow. Aronnax asks him, for Ned Land’s sake, if they could be allowed to return home. Nemo, angered, flatly refuses. Even so, The Nautilus begins to sail closer to land.
A large warship catches sight of The Nautilus floating on the surface and opens fire, even though Aronnax and his friends are on board. Aronnax realizes that when Ned Land struck The Nautilus with his harpoon so many months ago, the captain of the Abraham Lincoln must have heard the metal sound and told the world of the mysterious submarine vessel. Now the nations have teamed up to hunt a human enemy, not a narwhal. He also remembers the crewmember they buried in the coral, and realizes this is not the first time since he and his companions boarded The Nautilus that a warship has attacked them.
Nemo tells Aronnax and his companions to get below while he attempts to sink the warship. Aronnax pleads with Nemo to just submerge — The Nautilus could easily elude the warship’s guns — but Nemo refuses, blaming the enemy crew for the death of his own family. Once Aronnax sees Nemo’s hatred for the unknown men in the warship, he finally agrees to attempt to escape with Ned and Counseil. They plan to jump ship once The Nautilus gets closer to the warship, but they are trapped again when The Nautilus submerges. Nemo drives The Nautilus through the hull of the warship, sinking it and drowning the crew.
The whole crew, including Nemo, feels the horror of these events. Ned and Aronnax finalize plans of escape. The night they attempt it, however, The Nautilus floats into a mighty maelstrom near Norway. The lifeboat is torn from the vessel. Aronnax hits his head and is knocked out. When he wakes, he, Ned and Counseil have found shelter with a fisherman. As they wait for a boat that can take them to France, Aronnax calculates that they had traveled about 20,000 leagues with Captain Nemo. No one knows what happens to The Nautilus, or whether Nemo still lives. Aronnax hopes that if he lives, the wonders of the ocean will quell his vengeful spirit and he will die in peace.