In 1799, the captain of a sealing ship Bachelor’s Delight, Captain Amasa Delano, spots another ship drifting towards the bay of Santa Maria. Wondering if the ship is in distress, Delano boards his whale-boat and sets sail towards the suspicious ship. He learns that the ship is called the San Dominick, captained by Don Benito Cereno. Upon arrival, Delano is greeted by Spaniards and black men and women who beg him for water and supplies. Delano is troubled by the amount of black people on board since they greatly outnumber the Spaniards. This disparity is explained by the collective cries of those on-board, claiming that they had been hit by a fever that killed more of the Spaniard crew than of the slaves. Assuming the standard roles of the races, Delano ignores many troubling signs.
The ship is actually filled with rebel slaves who killed their owner, Alexandro Aranda, and are in control of the Spaniards and Captain Benito. Captain Benito is constantly served by Babo, the leader of the rebellion, and Delano does not suspect anything despite the fact that Benito is never left alone. Under Babo's control, Cereno claims he headed toward the Bolivian coast in order to acquire more hands on deck. Due to all of the aforementioned conditions, the ship has doubled its path several times. When Delano asks about the slaves' master, Alexandro Aranda, Benito states that he took fever aboard the ship and died.
Delano is disturbed by the incidents he observes, such as when a black boy slashes the head of a white boy with a knife. Surprisingly, Cereno does not acknowledge or even seem to care about this behavior. The whispered conversations between Cereno and Babo make Delano feel uncomfortable. Gradually, his suspicions increase as he notes Cereno's sudden waves of dizziness and anxiety, the crew's awkward movements and hushed talks, and the unusual interaction of the slaves and the crew. 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 dinghy arrives with supplies, Delano sends the dinghy back for more water while he continues to observe curious incidents.
Babo reminds Cereno that it’s time for his shave and suggests that Delano join them. Their suspicious behavior continues when Babo searches "for the sharpest" razor and Cereno "nervously shuddered" at the "sight of gleaming steel." Just when Delano asks Cereno how he spent over two months crossing a distance Delano himself would have sailed within a few days, Babo nicks Cereno's neck and draws blood. It is unclear whether the nick is caused by a sudden wave on the sea, or "a momentary unsteadiness of the servant’s hand." Delano feels that slavery fosters ugly passions and invites Cereno for coffee aboard the Bachelor’s Delight. Cereno declines the offer, offending Delano, who is increasingly irritated by the lack of opportunity to have a private conversation without Babo within hearing distance.
When the American steps into the dinghy and takes off, Don Benito jumps into the boat, falling at the feet of Captain Delano. Three Spanish sailors dive after him along with Babo, who is holding a dagger. Delano fears Babo wants to attack him, but he loses the dagger when he falls into the boat. With a second dagger, Babo attempts to stab Don Benito. Delano’s men prevent him from achieving his purpose. Delano finally realizes that a slave revolt has been going on aboard the San Dominick. The remaining sailors taking flight into the masts to escape 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; Delano's men 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. As Delano approached, the revolting slaves set up the illusion that the surviving whites are still in charge. Delano asks the sad Benito: "’you are saved; what has cast such a shadow upon you?'" To which Cereno replies: "The negro."
Some months after the trial, Babo is executed never having said a word to defend himself. His body is burned but his head is fixed on a pole in the Plaza. Babo's head looks 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."
