Un joven desarraigado pero de esmerada educación se embarca en un buque de carga en la Isla de Java. El viaje es accidentado y en el transcurso de una tormenta toda la tripulación, salvo el joven y un viejo marino, es arrojada al mar. Más tarde el navío será embestido por otro extraño barco de mucho mayor tonelaje. El joven logra salvarse encaramándose a la cubierta del mismo y se encuentra con una tripulación tan extraña como el propio barco. Éste avanza a toda vela, sin rumbo conocido, hasta que se precipita el fantástico desenlace.
An unnamed narrator, estranged from his family and country, sets sail as a passenger aboard a cargo ship from Batavia (now known as Jakarta, Indonesia). Some days into the voyage, the ship is first becalmed then hit by a Simoon (a combination of a sand storm and hurricane) that capsizes the ship and sends everyone except the narrator and an old Swede overboard. Driven southward by the magical Simoon towards the South Pole, the narrator's ship eventually collides with a gigantic black galleon, and only the narrator manages to scramble aboard. Once the new ship arrives, the narrator finds outdated maps and useless navigational tools throughout the ship. Also, he finds it to be manned by elderly crewmen who are unable to see him; he steals writing materials from the captain's cabin to keep a journal (the "manuscript" of the title) which he resolves to cast into the sea. This ship too continues to be driven southward, and he notices the crew appears to show signs of hope at the prospect of their destruction as it reaches Antarctica. The ship enters a clearing in the ice where it is caught in a vast whirlpool and begins to sink into the sea.