The story begins in the year 1866, when ships of several nations spot a mysterious sea monster.

The United States government assembles an expedition in New York City to find and destroy the monster.

Professor Pierre Aronnax, who happens to be in New York at the time, receives a last-minute invitation to join the expedition which he accepts.

The expedition departs Brooklyn aboard the United States Navy frigate Abraham Lincoln and travels south around Cape Horn into the Pacific Ocean.

The ship finds the monster after a long search and then attacks the beast, which damages the ship's rudder.

The three protagonists are then hurled into the water and grasp hold of the 'hide' of the creature, which they find, to their surprise, to be a submarine very far ahead of its era....