Benito Cereno is the story of a meeting between two ships in the Atlantic. The Bachelor's Delight and the San Dominick come alongside one another so that the former can offload relief supplies to the storm-battered latter, only to discover that the San Dominick has been seized by rebel slaves hiding behind a captive white crew. The novel meditates on violence, human connection, and depravity before the uprising is overthrown and its leader put to death, an event which occasions paradoxical sympathy in his victims.
Off the coast of Chile on one gray day in 1799, the sky filled with shadows "foreshadowing deeper shadows to come", captain Amasa Delano of the Bachelor's Delight , a Massachusetts sealer and trading ship, sees the Spanish vessel San Dominick in seeming distress. With some supplies he steps in his boat "The Rover" and boards the San Dominick , which carries a cargo of slaves, including women and children. He notes the figurehead, which is mostly concealed by a tarpaulin revealing only the inscription: "Follow your leaders and the fate of the slaves' master, Alexandro Aranda, who Cereno claims took fever aboard the ship and died. He sends his men back to bring more food and water, and stays aboard in the company of its Spanish captain, Don Benito Cereno and his Senegalese servant Babo who never leaves him alone. Don Benito’s timidness and the wild behavior of the slaves confuse Delano.
The San Dominick, Cereno informs him, is on a voyage from Buenos Aires to Lima with three hundred slaves and a crew of fifty Spaniards, but storms and diseases have decimated the crew. Cereno is constantly attended to by his personal slave, Babo, whom Cereno keeps in close company even when Delano suggests that Babo leave the two in private to discuss matters that are clearly being avoided. Delano, however, does not bother Cereno to ask questions about the odd superficiality of their conversation Delano, who appreciates Babo’s faithful care for his master, offers to help out by letting three of his own men assist in bringing the ship to Concepcion.
What disturbs Delano are incidents he observes among the hatchet polishers, oakum pickers, such as when a black boy stabs a white one. Apparently Cereno does not care about this behavior, not even when Atufal, a regal-looking slave appears in chains but still refusing to humble himself. The whispering between Cereno and Babo makes Delano feel uncomfortable. Gradually his suspicions increase, as he notes Cereno's sudden waves of dizziness and anxiety, the crew's awkward movements and whisperings, and the unusual interaction of the slaves and the whites. Yet Delano answers Cereno’s questions about the crew, cargo, and arms aboard the Bachelor’s Delight without reserve, reasoning that the innocent are protected by the truth. When The Rover arrives with the supplies, Delano sends her back for more water while he continuous to observe curious incidents.
Babo reminds Cereno that it’s time for his shave. "Most negroes are natural valets and hairdressers; taking to the comb and brush congenially as to the castinets, and flourishing them apparently with equal satisfaction," springing from "the docility arising from the unaspiring contentment of a limited mind." Babo suggests that Delano joins them in the cuddy to continue the conversation with Cereno, and Delano witnesses the shaving with an appreciative eye for Babo’s graceful skill as a barber and a hairdresser. Babo first searches "for the sharpest" razor, and Cereno "nervously shuddered" at the "sight of gleaming steel." Delano himself, for a brief moment, cannot resist "the vagary, that in the black he saw a headsman, and in the white, a man at the block." Cereno is nervously shaking, and just when Delano curiously asks him how he could have spent over two months crossing a distance Delano himself would havesailed within a few days, then, whether caused by a sudden wave on the sea, or "a momentary unsteadiness of the servant’s hand; however it was, just then the razor drew blood", and immediately "the black barber drew back his steel."
Delano precedes the two out of the cuddy and walks to the mainmast, where Babo joins him, complaining that Cereno cut his cheek in reproach for his carelessness, while Cereno’s own shaking caused the cut. Delano feels that slavery fosters ugly passions, and invites Cereno for coffee aboard the Bachelor’s Delight, which Cereno declines, offending Delano, who is also increasingly irritated by the lack of opportunity to have a private conversation without Babo within hearing distance.
When the American steps into The Rover and takes off, "Don Benito sprang over the bulwarks, falling at the feet of Captain Delano". Three Spanish sailors dive after him, just as Babo, "dagger in his hand", and a dark avalanche of slaves. Delano fears Babo wants to attack him, but the black loses the dagger when he falls into the boat. With a second dagger Babo continues his attack and now his purpose is revealed: "Not Captain Delano, but Don Benito, the black, leaping into the boat, had intended to stab." Delano’s men prevent him from achieving his purpose. Delano, "now with the scales dropped from his eyes", realizes that a slave revolt has been going on aboard the San Dominick. He sees the remaining sailors taking flight into the masts to escape the "flourishing hatchets and knives" of the blacks who are after them. The canvas falls off the ship's figurehead, revealing the strung-up skeleton of Alexandro Aranda. Delano secures Babo, and his men under command of his chief mate attack the Spanish ship to claim booty by defeating the revolting slaves.
Eventually, legal depositions taken at Lima explain the matter. Instead of storm and epidemics, a bloody slave revolt under Babo’s command caused the mortalities among the crew, including Aranda. When Delano approached, the freed slaves set up the delusion that the surviving whites were still in charge. Delano asks the sad Benito: "’you are saved; what has cast such a shadow upon you?’" To which Cereno replies: "’Thenegro.’"
Some months after the trial Babo is executed, never saying a word to defend himself: his body was burned but his head, "fixed on a pole in the Plaza, met, unabashed, the gaze of the whites", and looked in the direction of St. Bartholomew’s church, where "the recovered bones of Aranda" lay, and further across the bridge "towards the monastery on Mount Agonia without: where, three months after being dismissed by the court, Benito Cereno, borne on the bier, did, indeed, follow his leader."