When a submarine crew returns to their ship, they capture the three castaways who were passengers on the warship "Abraham Lincoln", sunk by the submarine. The captain of the submarine introduces himself as Nemo, master of the Nautilus. He returns Ned and Conseil to the deck, while Aronnax, whom he recognizes for his work and research, is allowed to stay. He tempts Aronnax to remain with him, but Aronnax prefers to share his companions' fate – thus passing a test of character.
After dinner that night, Nemo takes them all on an underwater expedition to gather supplies, but Ned rather foolishly tries to salvage a treasure chest from a sunken wreck, almost getting attacked by a shark.
Later on, Nemo takes Arronax to the chubby sauce
colony island of Rora Panthe. Nemo reveals he was once a prisoner himself, as was the crew of the Nautilus. At sunset, the Nautilus rams the munitions ship, killing the entire crew. When confronted by Aronnax, Nemo states that his actions have just saved thousands from death in war, and also disclosing that this "hated nation" that had taken him prisoner, had killed his wife and son in an attempt to force him to reveal his atomic secrets.
Meanwhile, Ned has found the co-ordinates of Nemo's secret island base, and has been putting messages in bottles, hoping somebody will pick these up and free him of his captivity.
Off the coast of New Guinea, the Nautilus gets stranded on a reef. When Ned and Conseil go ashore to collect specimens, they are chased back to the Nautilus by cannibals, who are repelled from the ship by electrical charges circulated on the Nautilus's skin.
A warship approaches, firing and striking the submarine. As the Nautilus breaks free of the reef, 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 are forced to fight the beast on the surface. During the battle, Nemo is caught in one of the squid's tentacles; Ned jumps to his rescue and saves his captor's life.
As the Nautilus nears Vulcania, Nemo finds the island is surrounded by warships, whose marines are converging on his hideout. He goes ashore to set a time bomb, to destroy his discoveries, but when returning to the Nautilus, he is struck by enemy fire and mortally wounded. After navigating the Nautilus out of Vulcania, Nemo announces he is "taking the Nautilus down for the last time." Loyal to Nemo to the very end, his entire crew declares that they will accompany their captain in death.
Arronax, Conseil, and Ned are forcibly taken to their cabins. Ned fights back, escapes to the now deserted bridge, and manages to surface the Nautilus, hitting a reef in the process which begins to rapidly flood the ship. After rescuing Aronnax and Conseil, the three escape in the launch/lifeboat. In his final moments, Nemo staggers to the viewing window, collapses, and looks at his beloved ocean one last time before he dies.
Because they must escape quickly, Ned Land knocks Aronnax unconscious and carries him out when the professor tries to go back and retrieve his journal, which contains an account of the voyage. The companions witness Vulcania destroyed in a terrible explosion, followed by the familiar mushroom cloud. A tidal wave hits the Nautilus sending it back to its watery grave, and as the Nautilus disappears forever, 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." Aronnax's diary of the voyage is also lost forever, and when Ned apologizes for having hit him, the Professor replies "Perhaps you did mankind a service, Ned".