Aboard the Nellie, anchored in the River Thames near Gravesend, England, 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. He describes his passage on ships down the African coast and then into the interior to the Company's Outer Station, which strikes Marlow as a scene of devastation: it is immensely disorganized, machinery parts scattered here and there; demolition explosions serving no apparent purpose are carried out periodically; native black men are chained together, wasted, demoralized, and literally being worked to death, and strolling beside them is another native working as a uniformed guard, carrying a rifle. At this station Marlow meets the Company's chief accountant who tells him of a Mr. Kurtz, explaining that Kurtz is a widely respected, first-class agent who brings in more ivory for the Company than all the other agents combined.
Marlow departs with a caravan to travel on foot some two hundred miles deeper into the wilderness to the Central Station, where the steamboat that he is to captain is based. When he arrives, he is shocked to learn that his steamboat had been wrecked two days earlier. The manager explains that they had tried to take the steamboat up-river because of rumours that an important station was in jeopardy and that its chief, Mr. Kurtz, was ill. Marlow describes the Company men at this station as lazy, back-biting "pilgrims", fraught with envy and greed, all trying to gain a higher status within the Company, which, in turn, would provide more personal profit; however, they seek these goals in a meaningless, ineffective and lazy manner, and Marlow senses that they are all merely waiting, while trying to stay out of harm's way. After fishing his boat out of the river, Marlow is frustrated by the months it takes to perform the necessary 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). Not only is Kurtz's position at the Inner Station highly envied, but sentiment seems to be that Kurtz is undeserving of it, as he received the appointment only through his European connections.
Once underway, the journey up-river to Kurtz's station takes two months to the day. On board are the manager, three or four "pilgrims" and some twenty indigenous "cannibals" enlisted as crew. 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 eight miles 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 pilgrims fire blindly into the bush with their Winchester rifles, and the native serving as helmsman gives up steering to pick up a rifle and fire it. Marlow grabs the wheel to avoid snags in the river. 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 watch the helmsman die, and Marlow forces the pilgrim to take the wheel so that he can fling his blood-soaked shoes overboard. Marlow and the rest of the crew presume (wrongly) that Mr. Kurtz is dead. 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, states "Exterminate all the brutes!" Marlow expresses that he does not believe Kurtz was worth the lives that were lost in trying to find him. After putting on a pair of slippers, he returns to the wheel-house and resumes steering. By this time the manager is there, and expresses a strong desire to turn back, but at that moment the Inner Station comes into view.
At Kurtz's station Marlow sees a man on the riverbank waving his arm, urging them to land. Because of his expressions and gestures, and all the colourful patches on his clothing, in between which possessions are shuffled, the man reminds Marlow of a harlequin. The pilgrims, heavily armed, escort the manager on to the shore to retrieve Mr. Kurtz. The harlequin-like man 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, through a telescope, 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. She raises her arms above her head and then walks back into the bushes. Marlow overhears Kurtz arguing with the manager, claiming his work at the Inner Station is not yet finished and that the Company is interfering with his plans. 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 he believes the Company wants to kill him and remove Kurtz from the station, and Marlow confirms that hangings had been discussed. The Russian then informs Marlow that Kurtz had ordered the natives to attack the steamer, hoping the men from the Company would abandon their mission to remove him. The Russian insists that he must leave immediately, referring to a canoe waiting for him, and before he departs he notes how delightful it was to hear Kurtz recite poetry.
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. Marlow appreciates his serious situation, and when Kurtz begins in a threatening tone, Marlow interjects that his "success in Europe is assured in any case"; at this, Kurtz allows Marlow to carry him back to the steamer. 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 himself 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!" Marlow blows out the candle and tries to act as though nothing has happened when he joins the other crew members for dinner. A short while later, the "manager's boy" appears and announces in a scathing tone: "Mistah Kurtz - he dead." The next day Marlow pays little attention to the pilgrims as they bury "something" in a muddy hole. He falls very ill, himself near death.
Upon his return to Europe, Marlow is embittered and contemptuous of the "civilized" world. Many callers come to retrieve the papers Kurtz had entrusted to him: Marlow offers the report entitled "Suppression of Savage Customs" (with the postscriptum torn off) to a representative of the Company, knowing that he is really looking for papers that might disclose the whereabouts of ivory rather than a humanistic treatise, but the man refuses the document. To another man, who claims to be Kurtz's cousin, Marlow gives family letters and memoranda of no importance. He then gives the 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". 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, which in fact are "The horror! The horror!". Uncomfortable, Marlow lies and tells her that Kurtz's final word was her name.