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In the seventeenth century, the pirate Captain Providence roams the waters of the Caribbean in the Sheba Queen and plunders British ships.  Unknown to the British seafarers who fear her, Captain Providence is a hard-fighting and proud woman named Anne who hates the English because they hanged her brother.

One day, Anne and her crew, including first mate Red Dougal, capture a British ship, and after forcing the crew to walk the plank, discover that the ship was carrying a French prisoner.  The man, Pierre, explains that he was the master of the Irish privateer the Molly O'Brien, and that he was being sent to England for trial.  Although Dougal distrusts Pierre, Anne decides to make him her sailing master.

Later, the Sheba Queen puts into Nassau and Anne introduces Pierre to the infamous pirate Blackbeard, who reared her and her brother after they were orphaned.  Blackbeard adores his fierce protégée, although like Dougal, he is unsure of Pierre.

That evening, Pierre slips away and does not return to the ship until late.  Fearing that Pierre is a spy, Anne orders him to be flogged.  Jameson, the ship's alcoholic doctor, tells Anne to stop the punishment and reveals that when he searched Pierre's cabin, he discovered half of a treasure map.  Anne excitedly declares that the map will lead to the loot of infamous pirate Henry Morgan, which Pierre confirms.  Pierre relates the map's history and tells Anne that the other half is at Port Royal, Jamaica, the stronghold of the British forces.

Anne hides the ship in a secret cove for repairs; there, she begins a romance with Pierre.  They are interrupted by the arrival of Blackbeard, who accuses Pierre of being Pierre François La Rochelle, an officer in the French Navy.  Pierre assures Anne that he was cashiered out of the Navy in disgrace and that he will serve her loyally.  Anne believes Pierre and strikes Blackbeard across the face after he stabs Pierre.  Warning Anne that he never forgets an insult, Blackbeard retreats, and Jameson tends to Pierre.

Later, by the time the Sheba Queen reaches Jamaica, Pierre has recovered and Anne has fallen in love with him.  Pierre insists on entering Port Royal alone to obtain the map, and once there, goes to The Governors' Tavern.  There, Pierre relates to the British Naval officers for whom he is spying that Captain Providence is a woman, and that her ship is within reach.  The officers, who have been holding Pierre's ship while he completed his forced mission to find Captain Providence, will not release the Molly O'Brien until Anne is captured, but in the meantime, Pierre is reunited with his wife Molly.

Dougal, who has followed Pierre, rushes back to the Sheba Queen and informs Anne that her lover is a married spy who has led her into a trap.  Anne escapes and vows revenge, while Pierre is informed by the British that his ship will not be returned because Anne was not captured.  Wherry offers to return the Molly O'Brien to Pierre if he turns pirate for the British and shares his spoils, but Pierre refuses until he learns that Anne has kidnapped Molly.  Pierre's ship is outfitted with a crew of gold-hungry swabs and they begin their pursuit of the Sheba Queen.

Meanwhile, a drunken and heartsick Anne confronts Molly with the information that she will be sold at the slave market in Maracaibo.  At the market, Anne is auctioning off Molly when Pierre's ship attacks the port.  Anne then ties Molly to the mast of the Sheba Queen so that Pierre will be forced to hold his fire.  Pierre's crew mutinies against his strange orders and a battle begins, during which Pierre jumps overboard and his ship is destroyed.  Anne then decides to strand Pierre and Molly on Dead Man's Cay without food or water.  She is plagued by nightmares after depositing her prisoners on the cay, and Jameson tells Anne that her conscience is punishing her for her cruel actions.  Remorseful at last, Anne returns to the cay and sends Jameson to Pierre and Molly with supplies.  Before Anne can leave, however, Blackbeard's ship arrives, and knowing that her former teacher will kill Pierre if he finds him, Anne orders her men to stand and fight in order to distract him.  As Pierre, Molly and Jameson watch the battle, they are amazed by Anne's foolhardy decision, for the Sheba Queen could easily outrun Blackbeard's heavier Revenge.  As the Sheba Queen sinks, they realize that Anne was doing the best she could to save them.  Moved by Anne's sacrifice, Pierre comforts Molly by assuring her that at last Anne is at home in the sea.