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The rather anti-social narrator heads to sea as a passenger on board a cargo ship leaving Java. He doesn't have any reason for going to sea besides a vague restlessness of the soul… and the fact that he doesn't seem to like anyone back on land.
A sudden hurricane hits the ship, which the narrator predicts and the captain ignores. This presumably doesn't help the narrator think better of people.
Everyone is washed overboard except the narrator and an old Swedish sailor who came aboard just before the ship left. Though they can keep the ship afloat, the two men are unable to pilot it, and the hurricane blows it towards the South Pole, which never means anything good.
They sail south for five days, drawn by the current and the winds. They survive by eating jaggeree (that's unrefined cane sugar to you non-19th century, folk) taken at great risk from the hull.
On the sixth day, the sun doesn't come up—major panic time—leaving them stranded in a black sea. They lash themselves to the mast and prepare for their seemingly inevitable doom.
Said doom arrives in the form of a giant black galleon, much older than their own ship and moving under full sail despite the hurricane winds.
It comes crashing down on top of them and sinks the already struggling vessel. The Swede is killed, but the narrator successfully leaps onto the galleon, unseen by the crew.
About that last part… the crew consists solely of old men speaking an unknown language and using outdated instruments. The narrator can't get any of the crew to give him the time of day, which doesn't exactly calm him down.
He decides to write down his story with paper stolen from the captain's quarters, then put the papers in a bottle and throw it into the sea just before he dies.
At least that way… well, we don't know what good that's gonna do, but he's gonna do it.
His fear subsides after a while (there's no sun, so he can't tell exactly how much time has passed) but he still can't get the crew to react. He writes the word "DISCOVERY" in tar on one of the spare sails; the crew eventually raises the sail onto the mast, without taking notice of the word.
The ship heads further south, with waves rising higher and higher into the air.
Things are getting seriously dicey. They come dangerously close to sinking the ship, but it always seems to escape at the last minute.
The narrator thinks this is because they're caught in a powerful current, which he calls the only "natural" explanation. Supernatural explanations are apparently a bit too freaky to express.
Great walls of ice crop up along either side of the ship, which help him overcome his previous fears for reasons passing understanding.
The narrator admits that he's interested in seeing what this weird crew is so interested in reaching. Wherever they're going, they seem pretty pumped to get there.
The ship arrives at its destination—a giant whirlpool at the South Pole—and gets pulled down. The narrator goes down with the ship after hastily scribbling his shrieks of horror on the paper and stuffing it in the bottle.