The story starts from the depiction of Captain Amasa Delano - a sea captain from Massachusetts. He is skilled enough to be entrusted a big ship with the very valuable cargo on board. We see his ship staying in the St. Maria harbor and the Captain just socializing with his crew, resting before the new sail. Suddenly he sees another ship coming to the harbor. The ship looks like the Ghost Ship: with torn sails and damaged wood. Captain Delano decides that he shall investigate what happened with the ship and aid the crew if someone has survived there. Some of his most trusted crew members and friends volunteer to go with him and the men board the boat and sail to the mysterious ship.
When Delano and his friends get on board they see that the ship isn’t abandoned. The crew is still there, though halved by a storm, fever that raged on board and finally by a shipwreck. Along with the crew there are lots of other people: starved and exhausted African slaves that the ship transferred to the slave market. The crew members are barely standing on their feet, but they manage to escort Captain Delano to their leader, a Spaniard named Benito Cereno.
Benito still bears the signs of his former luxurious life, but now he is as miserable as everyone else on board. The only person that helps him function is his faithful slave named Babo. Babo follows Benito everywhere, aiding him constantly. Captain Delano can’t get rid of the strange feeling that Benito Cereno isn’t the one he pretends to be, but he can’t understand who or what he is impersonating and why does Benito want to deceive him.
Benito Cereno tells Delano the story of the ship: her name was San Dominick and she was obviously a slave ship. She was bound for Lima, but numerous misfortunes made the crew seek sanctuary in the harbor, closest to them - St. Maria’s. Major storms made the crew to throw out everything, even food and water, just to stay afloat. When the fever killed a huge part of the team, Benito gave order to free slaves from their chains to let everyone work for the common survival. This move helped the crew of San Dominick reach the harbor relatively safely, not losing crew members anymore.
Delano sends his own crew back to his own ship to bring some extra food and water supplies he had on board, thinking that he is morally obliged to help the people after such miseries. Benito rejoices and emotionally thanks the Captain, but Babo strictly (maybe too confidently for a slave) tells him to stay calm and quiet, because it is dangerous for his master to get excited so much after the recent fever. While waiting for his crew to return, Delano looks around, observing some strange things around the ship he can’t explain. He sees that one of the slaves hits a Spaniard cabin boy with a knife, but Benito (who should clearly see it) pretends that it just didn’t happen and he didn’t notice anything. Delano starts his little investigation, walking around and talking to the crew. For the short time he learns that the slaves were the property of the friend of Benito Cereno - another Spaniard named Alexandro Aranda. Aranda died recently because of the fever, or so the crew says. Delano grows suspicious. He wants to know if the body of the deceased Alexandro is still on board, to understand if the version about fever is true or Aranda was simply killed. But he can’t openly ask such a rude question, showing his suspicions, so he has to ask Benito lots of additional questions to learn the truth.
One of the slave members of the crew, a black man named Atufal, enters, interrupting the conversation of Cereno and Delano. Cereno asks with surprise, if Atufal is ready to ask for pardon. Atufal, clearly exhausted and barely lifting his heavy chains, remains silent. Delano, who believes that the slaves are the humans of the same kind as their masters, is very impressed by Atufal’s willpower, resolve and nobility. In the meantime it is Benito’s turn for interrogation. He starts to ask a lot of very precise questions, like the size of the crew on Delano’s ship, the quality and quantity of their weapons. It can be anything from plain curiosity to the secret plan to take over Delano’s ship.
While the conversation continues, more strange things continue to happen around. With the corner of his eye Delano sees the sailor, holding something shiny, coming to them. Two of the slaves suddenly rush to him and press him to the ground. Benito again pretends that everything is fine - or just is too busy coughing - raising Delano’s suspicions even more. One of the non-slave members of the crew, who is tying the knots near Delano, tries to tell something to the Captain, but Delano can’t decipher the secret message. Moreover, they don’t have enough time to talk, because another slave leads the sailor away. Delano understands that something is very wrong on the ship, but still can’t understand what exactly.
Delano starts to press Benito, making them reveal more details about their travel and trying to catch him on lie. Benito comes up with new and new versions, saying some vague things about Cape Horn. When Cereno is cornered, Babo comes to the aid, gently reminding that it is time for the daily shave for his master and takes Benito away. While Benito is shaved, Delano stubbornly tries to resume the interrupted talk, asking about Cape Horn again. But before Benito answers, Babo accidentally slightly cuts him with the razor. Delano understands something about Babo, being the one who hides a mystery, but still can’t get all the puzzle pieces together. Soon he is invited for lunch with Benito and now Cereno isn’t in the proper mood to answer any questions. Moreover, he insists on being with Babo all the time, despite all the attempts of Delano to have a talk with him privately.
After the crew delivers the food and fresh water, Delano, feeling that something ominous is happening here, decides to leave San Dominick and never return. He asks to prepare a small boat he can use alone to get back to his own ship. The ship is lowered into the water, but when Delano takes his leave, something strange happens. Benito Cereno jumps aboard, like he is saving his life. Before Delano can react, Babo also jumps aboard after his master and tries to stab Delano. His men manage to protect their Captain, but suddenly Delano realizes that Babo wasn’t there for him, he tried to kill his master, Benito Cereno. Delano and his crew leave San Dominick, but when they are far enough, they see how a big piece of old canvas that covered the figurehead is blown away by the strong wind. There is a hanged skeleton on the figurehead, and the mysterious words written near the skeleton: “Follow your leader”.
The story narrative shifts to the court documents telling the ending of the story in dry and official words. We learn that there was a slave revolt on San Dominick, led by the two slaves we already know: Babo and Atufal. Alexandro Aranda, the slave owner, was killed during the revolt. He was the skeleton hanging from the figurehead, as a reminder for the rest of the crew to stay obedient, or they would follow their leader. Benito Cereno was spared, because he was the only one alive who was able to steer and navigate the ship. Babo wanted him to lead the ship towards Senegal, where the slaves hoped to leave San Dominick and disappear. The storms and fever interrupted his plan, so, when they were heading to St. Maria harbor, Babo suggested the new plan: Benito would pretend to be the slave master and he, Babo - his faithful slave, to be near him and control the Spaniard, preventing him from spoiling the initial plan.
The narrative returns to the present, showing the readers the trial. Babo and the rest of the revolted slaves are condemned to death and their heads are mounted to the poles as the warning to the other slaves. Benito Cereno dies soon of his illness, sad that there is no Babo around who, despite being a rebel, really knew how to treat it.