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Frederic Baptiste, a gentleman pirate, captures yet another ship belonging to Alexander Narbonne, the wealthy New Orleans shipping magnate, not realizing that among his booty is a stowaway from Boston named Deborah McCoy, who is disguised as a cabin boy.  Rather than being put on a lifeboat with the other passengers, Deborah is kept aboard the pirate ship, where she soon attracts Baptiste's attention.  When the pirate threatens to maroon her on a small island, Deborah slips ashore while his ship is docked in New Orleans, and is soon hired as an entertainer by Madame Brizar, the proprietor of a "School for Genteel Young Ladies."

After months of training, Deborah is finally sent out on her first assignment, a party held by Captain Robert Kingston, the head of the Seaman's Fund.  Deborah is surprised to discover that Robert and Baptiste are one and the same, but she agrees to keep his secret when she learns that Robert has been using his plunder from Narbonne's ships to support the local seamen.  In actuality, Robert killed the real Baptiste, who had been hired by Narbonne to destroy the competition, and now pretends to be the pirate in order to raise money to rebuild the local fleet.  Robert's ruse is discovered by Narbonne when his thugs steal the sea captain's ring.  With the help of Patout, his secretary, Narbonne sets a trap for Robert, not knowing that Deborah has overheard their plotting.

Later, Deborah gets into a fight with Robert's fiancée, Arlene Villon, the governor's niece, and becomes a fugitive from justice when Villon files assault charges against her.  Later, Robert returns to his ship and sets sail, unaware that Deborah is aboard, waiting for him.  When Deborah tells Robert what she overheard between Narbonne and Patout, he recognizes Narbonne's deception and changes course in order to attack the French ships that are actually carrying the shipping magnate's riches.

After months at sea, Robert successfully sinks Narbonne's three remaining ships, then heads back to New Orleans.  Deborah proclaims her love to Robert, but, as a man of honor, he rejects her, having already promised himself to Arlene.  Upon arriving in New Orleans, however, Robert learns that Arlene wed Narbonne during his absence, and is further shocked to learn that she sees her marriage merely as a convenience that should not interfere with their romance.  When Robert rejects her adulterous proposal, the infuriated Arlene agrees to help prosecute her ex-fiancé for piracy.  After Robert and his crew are arrested, the sea captain mistakenly believes that Deborah betrayed him.

Later, Narbonne offers Robert clemency if he agrees to sign a statement stating that all the money raised by the Seaman's Fund was from his looted ships, but the pirate refuses.  He then learns from Patout that it was Arlene who betrayed.  Robert and his men are then broken out of jail by Deborah and the local seamen, and the pirates set sail for distant waters, with Robert and Deborah happily united.