The unnamed narrator opens the story by telling us he's a jerky jerk from Jerksville. His family hates him, he couldn't care less about his country, and his primary hobby seems to be reading works of German philosophy just so he can point out mistakes in their arguments. Naturally, he heads to sea, where rude comments and surly dismissal of humanity goes with the turf, or surf, as it were.
He finds himself on a trading ship in the South Seas, pulled there by a nameless sense of the heebie-jeebies that later Poe heroes displayed in spades. His nerves prove well founded when he spots a cloud on the horizon, which soon turns into a hurricane (that's how weather works—didn't anyone tell you?). The storm blows the crew overboard, but the ship stays afloat, now populated only by the narrator and an old Swedish sailor who showed up right before the ship left port.
They sail on for five days, pulled south by the hurricane winds and feeling the air get colder by the minute. On the sixth day, the sun doesn't come up, leaving the two characters completely in darkness and presumably scared out of their wits. The waves grow larger and larger, threatening to engulf the ship at any moment. Then the Swede spots something incredible: a giant black ship, under full sail, hanging at the top of one of the waves. It crashes down on top of them, putting their own ship and the Swede out of their misery, but letting the narrator make a mighty leap onto the rigging.
A crew of old men pilots the black ship, using "mathematical instruments of the most quaint and obsolete construction." (19) They take no notice of the narrator, even when he steps right in the middle of them. They're too focused on heading as far south as they can. The narrator decides to write down what he has seen and put the message in a bottle, stealing paper and writing supplies from the captain's cabin to do so.
As scared as he is, he confesses to being just a little bit curious about where they're headed. He clearly hasn't read any Poe stories before. They eventually arrive at a giant black whirlpool at the South Pole, something the elderly crew eagerly looks forward to. The narrator feels somewhat differently about the matter ("Oh horror upon horror!" ), but he's stuck where he is as the ship tumbles down into the void, leaving behind only the bottle.