The French epigraph of the message translates to "He who has only a moment to live no longer has anything to hide." The narrator dismisses his country and family, saying only that they are estranged and that his family's wealth gave him an excellent education that taught him about the German moralists, whose "eloquent madness" amuses his logical and unimaginative mind. He says this because he wishes the reader to know that his story, although apparently fanciful, is not a fabrication but merely a truthful account of his experiences.
He describes a voyage that he took from Java on a ship headed to the Archipelago of the Sunda islands. He was on the ship as a passenger because of his restlessness and desire to travel, but the ship was unstably packed with cargo such as cotton-wool, unrefined sugar, coconuts, and opium. One evening, the narrator observes an isolated cloud in the distance, which spreads and coincides with a change in the water, a rise in temperature, and a calming of the wind. The captain decides that the conditions are safe, despite the narrator's worries of a special type of storm called a Simoom, and the narrator goes below deck. He cannot sleep, and when he goes to the deck, he sees the ship shake before a blast of foam overtakes the deck. The overburdened ship is driven underwater, but the sea's blast manages to right the boat.
When the storm is over, the narrator and the old Swede are the only ones who have survived the accident, as everyone else was either drowned in the cabins or dragged overboard. The ship is trapped in a whirlpool, and the two are unable to free it but manage to keep it from going under for five days, while they subsist on unrefined sugar. The ship heads in a southern direction, and by the fifth day, the weather grows cold, and the sun ceases to rise above the horizon.
The darkness prevents them from seeing anything, and they begin to neglect the ship and secure themselves to a mast to watch the ocean. The Swede is superstitious but hopeful, while the despairing narrator prepares for death as the ship is thrown in and out of the sea. They see a dull red light that heralds the arrival of a huge black ship on the crest of a wave. It descends on part of the smaller ship and throws the narrator onto the new ship's rigging. He sneaks into the hold, where he observes an extremely old man who speaks a foreign language.
The men on the ship are preoccupied and cannot see the narrator, who boldly goes into the captain's cabin and finds paper on which to write his account, which he plans to place in a bottle and throw into the sea. He recalls an incident when he idly used a tar brush on the edge of a folded sail. When the sail unfolded, the tar formed the word "discovery." He also observes the ship, which seems antiquated but vaguely familiar. The wood is porous - not very appropriate for a ship - and he remembers meeting a Dutch navigator who used to say, "It is as sure as sure as there is sea where the ship itself will grow in bulk like the living body of the seaman."
The narrator joins the crew, who still do not see him and are all ancient and equipped with obsolete mathematical instruments. The ship heads due south into the extremely choppy waters, and the narrator goes below deck because unlike the crew, he cannot remain steady on the deck. He guesses that the ship can navigate these waters because it is following a strong current.
The captain, like the ship and his crew, is ancient, and he mutters to himself in a foreign tongue over his papers. The narrator feels them to be more eager than despairing, and he is ashamed of his worrying. He is frightened but curious to find new secrets in what he suspects will be the South Pole, but the ice parts to reveal a giant whirlpool that captures the ship and forces it to sink.
The narrator begins "MS. Found in a Bottle" with the claim that he is not an especially imaginative person and that his inability to imagine such an unusual story means that the reader should take his words as truth. A man such as he has described would not normally be interested in the discovery of the fantastic, and he only books a passage on the ship on Java because he is driven by restlessness. He is prone to worrying about storms and later about his imminent death, and does not have the imagination necessary to emulate the old Swede and believe in hope. By the end of the story, he is eagerly awaiting the conclusion of his trip on the ship Discovery and is taking inspiration from the members of the crew to overcome his fear of his imminent destruction with curiosity and excitement. The details of the story are meant to highlight this transformation in the narrator's personality while also serving as an adventure tale.
In journeying toward the South Pole, the Discovery seeks what can be interpreted as forbidden knowledge, and the giant whirlpool that ends the narrator's story is representative of its forbidden nature. Just as the ship is about to reach its destination at the southern ends of the world, the ice opens as if to reveal its hidden contents, only to show that the crew's destruction is imminent despite their probable failure to uncover the mysteries for which they have overcome their despair. That the narrator could have journeyed so far and learned so much about his own capacity to overcome fear only to die without seeing his goal is ironic in the extreme. In this sense, the naming of the Discovery is misplaced and grimly humorous. The ancient men of the ship, who are in age very close to death, have prolonged their stay in life to see this new land, but in the end they succumb before reaching their destination.
An alternative explanation for the journey of the Discovery is that the ship's destination is not the South Pole, as the narrator surmised, but rather the realm of death, which has also remained unexplored. In this interpretation, the narrator's former fear of death has changed into the anticipation of discovering death, and in that respect, the abrupt end of the story is not one of ironic destruction but rather one of spiritual transcendence. The requirement of the plot is that the narrator must finish his manuscript and send it away before the ship sinks into the whirlpool, but more importantly, we cannot learn of his experiences because we still belong in life. Although the narrator will soon find out the answers to what lies after death, along with the crew, who have evidently chosen to take the symbolic rather than the aging route to destruction, the reader is not equipped to learn the answers.
According to the previous understandings of "MS. Found in a Bottle," Poe was describing the transformation of an unimaginative man into an intrepid explorer in the shadow of forbidden knowledge. However, a third explanation translates the story into a satire of seafaring travelogues and of John Symmes's theory that the earth is actually an elongated torus, with an inhabitable hole connecting the poles of the Earth. Poe gives the theory the straightforward treatment, but given the implausibility of Symmes's hypothesis, which Symmes attempted to prove by asking the United States navy to send an expedition, Poe may have been offering a tongue-in-cheek critique of Symmes's false science by having a whirlpool appear just before the narrator can confirm this model of the Earth.
"MS. Found in a Bottle" has been counted as one of the forerunners of the modern science fiction genre because it features a narrator who describes himself as pedantic and level-headed and thus gives credibility to the discovery of new knowledge. The story is fantastic, but the presence of a narrator who deals strictly with truth gives it the sense of science fiction, which often deals in semi-plausible speculation about what might be true. Simultaneously, Poe may also have undercut his account by making the narrator seem more given to hyperbole than he claims, given that the narrator indulges in fairly fanciful descriptions of the various storms and whirlpools through the story. Additionally, Poe displays clearly in his stories about C. Auguste Dupin that he values the combination of logic and creativity over the pure existence of reason, so "MS. Found in a Bottle" may be satirizing the "aridity" of the main character's intellect by juxtaposing it with elaborate descriptions of his experiences.