In the year 1868, rumors of a sea monster attacking ships in the Pacific Ocean have created apprehension and fear among sailors, disrupting shipping lanes. The United States government invites Professor Pierre M. Aronnax and his assistant, Conseil, onto an expedition to prove or disprove the monster's existence.
One of their fellow crew is the cocky master harpooneer Ned Land. After months of searching, the "monster" is spotted. Though the ship fires at it with cannons, the monster rams the ship. Ned and Aronnax are thrown overboard, and Conseil goes in after Aronnax.
The warship, burning and helpless, drifts silently and no one on board answers when the overboard passengers cry for help. The three drift in the ocean, eventually finding a strange-looking metal vessel, and realize the "monster" is a man-made "submerging boat" that appears deserted.
Inside, Aronnax finds a viewing window and sees an underwater funeral. Ned, Aronnax, and Conseil then attempt to leave in their lifeboat, but the submarine crew returns to their ship, capturing the castaways. The captain introduces himself as Nemo, master of the Nautilus.
He returns Ned and Conseil to the deck, while offering Aronnax, whom he recognizes for his work and research, the chance to stay. When Nemo determines that Aronnax would die with his companions, he allows Ned and Conseil to board the submarine.
Nemo takes Aronnax to the penal colony island of Rura Penthe. Nemo reveals he was once a prisoner there, as were many of his crew. The prisoners are loading a munitions ship. The Nautilus rams the ship, destroying its cargo and killing the crew.
An anguished Nemo tells Arronax that his actions have saved thousands from death in war; he also discloses that this "hated nation" tortured his wife and son to death while attempting to force him to reveal the secrets of his work.
Ned discovers the coordinates of Nemo's secret island base, Vulcania, and releases messages in bottles, hoping somebody will find them and free him from captivity. Off the coast of New Guinea, the Nautilus becomes stranded on a reef.
Ned is surprised when Nemo allows him to go ashore with Conseil, ostensibly to collect specimens. Ned goes off alone to explore avenues of escape. While kneeling at a pool to drink he sees a number of human skulls on stakes.
Realizing his danger, Ned runs for his life and rejoins Conseil as they are chased back to the Nautilus by cannibals. Despite remaining aground, Nemo is unconcerned and the cannibals are repelled from the ship by electrical charges circulated on its hull.
Nemo is furious with Ned for not following his orders, and confines him to the submarine's brig. A warship approaches, firing upon the submarine. It descends into the depths, where it attracts the attentions of a giant squid.
The electric charge fails to repel the monster, so Nemo and his men surface to dislodge the beast. Nemo is caught in one of the squid's tentacles. Ned, having escaped from captivity during the struggle, jumps to Nemo's rescue, saving his captor's life.
As a result, Nemo has a change of heart; he claims now to want to make peace with the outer world. As the Nautilus nears Vulcania, Nemo finds the island surrounded by warships whose marines are converging on his hideout.
As Nemo goes ashore, Ned attempts to identify himself as the author of the bottled messages. Aronnax realizes this and becomes furious, recognizing that Nemo will destroy all evidence of his discoveries.
Nemo plants a bomb in his hideout, but is mortally wounded from a slug to the back while returning to the Nautilus. After haphazardly navigating the submarine away from Vulcania, Nemo announces he will be "taking the Nautilus down for the last time".
Nemo's crew declare they will accompany their captain in death. Aronnax, Conseil, and Ned are confined to their cabins. The Nautilus's crew also retreat to their cabins at Nemo's instructions.
Ned breaks loose and manages to surface the Nautilus, hitting a reef in the process and causing the ship to begin flooding. Nemo staggers to a viewing window and watches his beloved ocean as he dies.
Aronnax tries to retrieve his journal, which contains an account of the voyage, but the urgency of their escape obliges Ned to knock him unconscious and carry him out. The companions witness Vulcania destroyed in an explosion, while Ned apologizes to Aronnax for hitting him.
As the Nautilus disappears beneath the waves, Nemo's last words to Aronnax echo: "There is hope for the future. And when the world is ready for a new and better life, all this will someday come to pass, in God's good time."