In the latter half of the 19th century, a mysterious sea creature wreaks havoc on the naval ships of various nations, leaving those that survive with massive triangular holes in their hulls. As maritime trade faces mounting threats, the United States dispatches the military frigate Blue Star on a mission to locate and eliminate the elusive monster.

The Nautilus reaches the coast of India, where the crew dons spacesuits for a seabed excursion, exploring pearl deposits. Their underwater journey takes an intriguing turn when local envoys visit the submarine, revealing the true identity of Captain Nemo as Prince Dakkar, a Hindu and former leader of the sepoy rebellion known as Nana Sahib, now a fugitive with a bounty on his head.

As the Nautilus nears Crete, it finds itself relentlessly pursued by an English frigate equipped with heavy artillery and depth charges, matching the submarine in speed. Aboard the frigate is Colonel Bunro, who, unlike Nemo, does not know his adversary but suspects a past encounter. Convinced of the Nautilus's destruction, Bunro sees its presence as a catalyst for burgeoning national liberation movements.