The Black Corsair decides to stealthily go to Maracaibo, led by Carmaux and Van Stiller, and take away his brother's body (The Red Corsair) to give him proper burial at sea. Carmaux, Moko, and the Black Corsair, in the company of Rum, a little monkey that took refuge in the corsair's hat and his arm to escape the attack of a predator, arrive at a local tavern, crowded with people who are taunting and laughing at men who are being hanged, rejoicing over their death.
The Black Corsair engages in a duel with a nobleman, runs his sword through him, and leaves the tavern; Moko knocks out the Spanish guard with his blowgun, and they then remove the body of the Red Corsair from its indecorous custody. The corpse is respectfully wrapped in the cloak of the Black Corsair. Even though, the Basques who were in the tavern are waiting to ambush them on their way back. Carmaux and the Black Corsair fend off the four Basques, armed with navajas, killing three of them, and letting the fourth wounded man run away, disappearing into the night.
Back on board the Thunderbolt, the Black Corsair and his crew along with Trinchetto, a little green pirate-talking parrot pay their last respects to the Red Corsair, entrusting his body to the waters of "Davy Jones Locker" where the Green Corsair (the younger brother who was also hanged by the villainous, cold, calculated, evil, sadistic, and ruthless main antagonist, Van Gould) is already resting. The Thunderbolt sails towards Tortuga, when one day, they spot a Spanish ship directed to Maracaibo. The Black Corsair decides to attack it.
A Flemish duchess is on board by the name of Honorata Willermann (Van Gould), Duchess of Weltendrem, whom the Black Corsair decides to take to the Tortuga for the purpose of asking his men for a large ransom in exchange for her release (as was customary in those days). But the Duchess is young, very beautiful, kind, and full of charm, and although he tries to restrain himself in every possible way, the Black Corsair falls in love with her. When they arrive at Tortuga, the Black Corsair informs the Duchess and goes out to sea again with his men, leading the powerful corsair fleet towards Maracaibo, where Van Gould, his mortal enemy, is expecting him. The Black Corsair is on deck, engrossed in his sad, thoughts. To his great surprise he sees the duchess coming towards him, and they at last confess the love they feel each other without reticence. It is then that the Corsair tells her his story: he is in fact a knight, Emilio of Roccabruna Seigneur of Ventimiglia. He and his three brothers had been sent as officers by the Duke of Savoy to reinforce the troops of Louis XIV in his war against Spain for the possession of Flanders.
They fought valiantly but the French and their Piedmontese allies advanced, scattering the Spaniards, pushing them back to Anversa. One ill-fated day, the regiment to which the four brothers belonged, was trying to occupy a stronghold when it was suddenly attacked by many enemies so many that they were forced to barricade themselves inside the walls. Cut off from the French Army, surrounded by an enemy ten times bigger, they had no choice but to surrender or die. But no one thought of surrendering. The command of the regiment was in the hands of an old Flemish Duke who had the reputation of being a brave and skilled warrior.
The elder brother of the Black Corsair had become the soul of the defense, impressing both his friends, and the enemies with his courage, but causing the secret jealousy of the Flemish commander, which would lead to terrible tragedies. In fact, the Duke, forgetting his honor and oath of allegiance, made a secret agreement with the Spaniards- in exchange for being appointed Governor of the American Colonies (along with a huge sum of money), the Duke promised to deliver the stronghold to them by clandestinely opening one of the doors during the night. The elder brother of the Corsair noticed the Spaniards were getting in and gave the alarm, but was killed by the traitor duke. The stronghold fell, and the three surviving brothers only barely managed to save themselves. Once the war was over, they spent a long time searching for the treacherous Duke in Flanders and in Spain.
Having learned that he had been appointed Governor of one of the towns of the Colonies, the three brothers, commanding three splendid ships, set sail for the Caribbean, driven by the desire to avenge their dead brother. They then became the Corsairs. The Green Corsair, who was more impetuous and less experienced, was the first to fall into the hands of their mortal enemy and be hanged. And the same fate was to later befall the Red Corsair. After resisting bravely, the town falls into the hands of the pirates. Among the wounded, they find the Spaniard who had guided them in the jungle on the trail of Van Gould. The Black Corsair and his friends take the Spaniard to the Thunderbolt, and there, they find Honorata who has been anxiously awaiting the Corsair's return. The Spaniard is left speechless, for what on earth is the daughter of the worst enemy of the Black Corsair doing on his ship? Honorata is the daughter of Van Gould, and the Black Corsair, tormented by grief, finds himself having to make the saddest decision of his life: for the sake of the oath he made to his dead brothers, he gives the order to abandon her at sea on a lifeboat.
When the boat later disappears in the night, Moko, Carmaux, Van Stiller, and the others each identify the Black Corsair to one another, in the midst of a storm. They sight him on the fore-bridge, holding his face in his hands, sobbing violently. A year has elapsed since the Black Corsair had abandoned Honorata at sea, and remorse and regret have not given him a moment's respite. He goes to Puerto Limon to speak to Van Gould's administrator, wishing to ask him for news of Honorata, because the girl is rumored to still be alive. Honorata had in fact been sighted on her lifeboat, two days after she had been abandoned, off the coast of Cuba.
The Black Corsair finds out that his mortal enemy has taken refuge in Veracruz, and the other famous Corsairs of the Tortuga have decided to help the him: they will attack Veracruz, so as to let the Black Corsair capture Van Gould. The Black Corsair and the others manage to get into the fort and to speak to Diego Sandorf. The latter tells him that Honorata was rescued by a ship, but that it had been struck by a hurricane, shipwrecked off the coast of Florida. The indigenous people had massacred the whole crew, but impressed with the appearance of the young duchess, they treated her with great respect.
The Black Corsair and his friends are then captured and transported onto a Spanish vessel, the Alhambra. The pirates of the Thunderbolt, aboard the Alhambra, release the Black Corsair and the others, abandoning the Spanish ship to the fury of the elements. In the meantime, the powerful frigate with Van Gould on board, has reached them. While a hurricane rages, the two enemies, in command of their ships do battle. Van Gould, like a madman, has lighted the powder keg and cries: "Die all of you!" He next jumps into the sea. The masts on one bridge of the Thunderbolt are blown up, and as the ship drifts away, propelled by the force of the hurricane. The Black Corsair and his friends hang on to the ship's debris, drifting with the current towards the coast of Florida.
They soon find themselves crossing the terrible marshes of Florida, but they are unfortunately captured by the indigenous people who resolve to kill them. In any case, the "Sea Spirit" will later decide their fate. They are then told that the "Sea Spirit" has declared them to be sacred and untouchable. The Black Corsair then dashes towards the veiled figure who has proclaimed their freedom, and discovers that it is in fact Honorata. At last, free from feelings of vengeance and hatred, the two lovers find each other again and embrace once more.