Aboard the Nellie, anchored in the River Thames near Gravesend, Charles Marlow tells his fellow sailors about the events that led to his appointment as captain of a river steamboat for an ivory trading company. As a child, Marlow had been fascinated by "the blank spaces" on maps, particularly by the biggest, which by the time he had grown up was no longer blank but turned into "a place of darkness" (Conrad 10). Yet there remained a big river, "resembling an immense snake uncoiled, with its head in the sea, its body at rest curving afar over a vast country and its tail lost in the depths of the land" (Conrad 10). The image of this river on the map fascinated Marlow "as a snake would a bird" (Conrad 10). Feeling as though "instead of going to the centre of a continent I were about to set off for the centre of the earth", Marlow takes passage on a French steamer bound for the African coast and then into the interior (Conrad 18). After more than thirty days the ship anchors off the seat of government near the mouth of the big river. Marlow, with still some two hundred miles to go, takes passage on a little sea-going steamer captained by a Swede. He departs some thirty miles up the river where his company's station is. Work on the railway is going on, involving removal of rocks with explosives. Marlow enters a narrow ravine to stroll in the shade under the trees, and finds himself in "the gloomy circle of some Inferno": the place is full of diseased Africans who worked on the railroad and now await their deaths, their sickened bodies already as thin as air (Conrad 24–25). Marlow witnesses the scene "horror-struck" (Conrad 26).
Marlow has to wait for ten days in the company's Outer Station, where he sleeps in a hut. At this station, which strikes Marlow as a scene of devastation, he meets the company's impeccably dressed chief accountant who tells him of a Mr. Kurtz, who is in charge of a very important trading-post, and a widely respected, first-class agent, a "'very remarkable person'" who "'Sends in as much ivory as all the others put together'" (Conrad 28). The agent predicts that Kurtz will go very far: "'He will be a somebody in the Administration before long. They, above—the Council in Europe, you know—mean him to be'" (Conrad 29).
Marlow departs with a caravan of sixty men to travel on foot about 200 miles (320 km) into the wilderness to the Central Station, where the steamboat that he is to captain is based. On the fifteenth day of his march, he arrives at the station, which has some twenty employees and is shocked to learn from a fellow European that his steamboat had been wrecked in a mysterious accident two days earlier. He meets the general manager, who informs him that he could wait no longer for Marlow to arrive, because the up-river stations had to be relieved and tells a rumour that one important station is in jeopardy because its chief, the exceptional Mr. Kurtz, is ill. "Hang Kurtz", Marlow thinks, irritated (Conrad 34). He fishes his boat out of the river and is occupied with its repair for some months, during which a sudden fire destroys a grass shed full of materials used to trade with the natives. While one of the natives is tortured for allegedly causing the fire, Marlow is invited in the room of the station's brick-maker, a man who spent a year waiting for material to make bricks. Marlow gets the impression the man wants to pump him and is curious to know what kind of information he is after. Hanging on the wall is "a small sketch in oils, on a panel, representing a woman draped and blindfolded carrying a lighted torch" (Conrad 39). Marlow is fascinated with the sinister effect of the torchlight upon the woman's face, and is informed that Mr. Kurtz made the painting in the station a year ago. The brick-maker calls Kurtz "'a prodigy'" and "'an emissary of pity, and science, and progress'", and feels Kurtz represents the "'higher intelligence, wide sympathies, a singleness of purpose'" needed for the cause Europe entrusts the Company with (Conrad 39). The man predicts Kurtz will rise in the hierarchy within two years and then makes the connection to Marlow: "'The same people who sent him specially also recommended you'" (Conrad 39–40).
Marlow is frustrated by the months it takes to perform the repairs, made all the slower by the lack of proper tools and replacement parts at the station. During this time, he learns that Kurtz is far from admired but more or less resented (mostly by the manager). Once underway, the journey up-river to Kurtz's station takes two months to the day. The steamboat stops briefly near an abandoned hut on the riverbank, where Marlow finds a pile of wood and a note indicating that the wood is for them and that they should proceed quickly but with caution as they near the Inner Station.
The journey pauses for the night about 8 miles (13 km) below the Inner Station. In the morning the crew awakens to find that the boat is enveloped by a thick white fog. From the riverbank they hear a very loud cry, followed by a discordant clamour. A few hours later, as safe navigation becomes increasingly difficult, the steamboat is attacked with a barrage of small arrows from the forest. The helmsman is impaled by a spear and falls at Marlow's feet. Marlow sounds the steam whistle repeatedly, frightening the attackers and causing the shower of arrows to cease. Marlow and a pilgrim (Marlow's word for the European hangers-on in the steamer) watch the helmsman die. In a flash forward, Marlow notes that the International Society for the Suppression of Savage Customs had commissioned Kurtz to write a report, which he did eloquently. A handwritten postscript, apparently added later by Kurtz, reads "Exterminate all the brutes!" (Conrad 83).
At Kurtz's station Marlow sees a man on the riverbank waving his arm, urging them to land. The pilgrims, heavily armed, escort the manager on to the shore to retrieve Mr. Kurtz. The man from the bank boards the steamboat and turns out to be a Russian wanderer who had happened to stray into Kurtz's camp. He explains that he had left the wood and the note at the abandoned hut. Through conversation Marlow discovers just how wanton Kurtz can be; how the natives worship him; and how very ill he has been of late. The Russian admires Kurtz for his intellect and his insights into love, life and justice and suggests that he is a poet. He tells of how Kurtz opened his mind and seems to admire him even for his power—and for his willingness to use it. Marlow, on the other hand, suggests that Kurtz has gone mad.
From the steamboat, Marlow observes the station in detail and is surprised to see near the station house a row of posts topped with the severed heads of natives. Around the corner of the house, the manager appears with the pilgrims, bearing a gaunt and ghost-like Kurtz on an improvised stretcher. The area fills with natives, apparently ready for battle but Kurtz shouts something from the stretcher and the natives retreat into the forest. The pilgrims carry Kurtz to the steamer and lay him in one of the cabins, where he and the manager have a private conversation. Marlow watches a beautiful native woman walk in measured steps along the shore and stop next to the steamer. When the manager exits the cabin he pulls Marlow aside and tells him that Kurtz has harmed the company's business in the region, that his methods are "unsound". Later, the Russian reveals that Kurtz believes the company wants to remove him from the station and kill him and Marlow confirms that hangings had been discussed.
After midnight, Marlow discovers that Kurtz has left his cabin on the steamer and returned to shore. He goes ashore and finds a very weak Kurtz crawling his way back to the station house, though not too weak to call to the natives for help. Marlow threatens to harm Kurtz if he raises an alarm but Kurtz only laments that he had not accomplished more in the region. The next day they prepare for their journey back down the river. The natives, including the ornately dressed woman, once again assemble on shore and begin to shout unintelligibly. Noticing the pilgrims readying their rifles, Marlow sounds the steam whistle repeatedly to scatter the crowd of natives. Only the woman remains unmoved, with outstretched arms. The pilgrims open fire as the current carries them swiftly downstream.
Kurtz's health worsens on the return trip and Marlow becomes increasingly ill. The steamboat breaks down and while it is stopped for repairs, Kurtz gives Marlow a packet of papers, including his commissioned report and a photograph, telling him to keep them away from the manager. When Marlow next speaks with him, Kurtz is near death; as he dies, Marlow hears him weakly whisper "The horror! The horror!" (Conrad 116). A short while later, the "manager's boy" announces to the rest of the crew, in a scathing tone, "Mistah Kurtz—he dead" (Conrad 117). The next day Marlow pays little attention to the pilgrims as they bury "something" in a muddy hole (Conrad 117). He falls very ill, himself near death.
Upon his return to Europe, Marlow is embittered and contemptuous of the "civilised" world. Many callers come to retrieve the papers Kurtz had entrusted to him, but Marlow withholds them or offers papers he knows they have no interest in. He then gives Kurtz's report to a journalist, for publication if he sees fit. Finally Marlow is left with some personal letters and a photograph of Kurtz's fiancée, whom Kurtz referred to as "My Intended" (Conrad 79). When Marlow visits her, she is dressed in black and still deep in mourning, although it has been more than a year since Kurtz's death. She presses Marlow for information, asking him to repeat Kurtz's final words. Uncomfortable, Marlow lies and tells her that Kurtz's final word was her name.