As the story begins in 1866, a mysterious sea monster, theorized by some to be a giant narwhal, is sighted by ships of several nations; an ocean liner is also damaged by the creature. The United States government finally assembles an expedition in New York City to track down and destroy the menace. Professor Pierre Aronnax, a noted French marine biologist and narrator of the story, who happens to be in New York at the time and is a recognized expert in his field, is issued a last-minute invitation to join the expedition, and he accepts. Canadian master harpoonist Ned Land and Aronnax's faithful assistant Conseil are also brought on board.

The expedition sets sail from Brooklyn aboard a naval ship called the Abraham Lincoln, which travels down around the tip of South America and into the Pacific Ocean. After much fruitless searching, the monster is found, and the ship charges into battle. During the fight, the ship's steering is damaged, and the three protagonists are thrown overboard. They find themselves stranded on the "hide" of the creature, only to discover to their surprise that it is a large metal construct. They are quickly captured and brought inside the vessel, where they meet its enigmatic creator and commander, Captain Nemo.