An unnamed narrator frames his story by disclaiming connection to his family and country. He says that he prefers the company of the German moralist writers, whose flights of fancy he can detect and repudiate. He admits having a rigidly rational mindset, dedicated to the truth and impervious to superstition.

The narrator then recounts a voyage from the island of Java upon a vessel containing cotton-wool, cocoa-nuts, and a few cases of opium. Soon after departure, the narrator observes a large, ominous cloud in the distance and fears the signs of an approaching Simoom, or typhoon. The captain of the ship, however, dismisses the narrator’s fears. As he retreats below deck, the narrator hears a loud noise and feels the ship capsizing. When the ship bobs back up, the narrator realizes that he and an old Swede are the only survivors. However, the ship remains engulfed in a whirlpool, which threatens to suck the vessel into the depths of the sea. For five days, the two men float on the shattered ship, escaping the pull of the whirlpool. They find their surroundings have grown cold, and soon complete darkness overwhelms them.