strange giant "sea creature" has been rampaging the seas. The American naval ship Abraham Lincoln is sent to investigate, but is rammed by "the creature" which turns out to be The Nautilus, the fantastic submarine of the enigmatic Captain Nemo, and "Rudderless, the 'Abraham Lincoln' drifts on". Then, in "A strange rescue" he guides the sub to surface under those pitched overboard and his crew take them, including Professor Aronnax, and his daughter (who are French) below through a hatch in the surface of the deck. After they pledge not to escape, Nemo shows them the wonders of the underwater world, and even takes them hunting on the sea floor.

Meanwhile, soldiers in a runaway Union Army Balloon are marooned on a mysterious island not far from the submarine. They find a wild girl living alone on the island ("a child of nature").

The yacht of Charles Denver arrives at the island. A former Indian colonial officer, he has been haunted by the ghost of a woman (Princess Daaker) that he attacked years ago; she stabbed herself rather than submit to him. He fled with her young daughter and then abandoned the child on the island. The long-tormented Denver has returned to see what became of her.

One of the Union soldiers schemes and kidnaps the wild girl onto Denver's yacht. Another soldier swims aboard to rescue her. At the same time, Nemo discovers that the yacht belongs to Denver, the enemy he has been seeking all these years. The Nautilus destroys the yacht with a torpedo, but the girl and her rescuer are saved from the water by Captain Nemo.

In elaborate flashback scenes to India, Nemo reveals that he is Prince Daaker, and that he created the Nautilus to seek revenge on Charles Denver. He is overjoyed to discover that the abandoned wild girl is his long-lost daughter, but his emotion is such that he expires. His loyal crew bury him at the ocean bottom. They disband and the Nautilus is left to drift to its own watery grave.