In 1668 Jamaica, having escaped a failed honey trap set by the authorities, Morgan Adams hunts down her uncle and fellow pirate Dawg Brown after he kidnaps her father, Black Harry. Black Harry has one of three pieces of a map to a huge stash of gold on the remote Cutthroat Island. Dawg has another piece, having stolen it after betraying and murdering his younger brother Richard, while a fourth brother, Mordechai, has the last piece. Harry refuses to give Dawg his piece and escapes with Morgan's help. Dying from his wounds, Harry reveals to his daughter the location of the map piece: on his scalp.

After scalping her dead father for the piece, Morgan, now captain of her father's ship, the Morning Star, sets out to find the treasure. Unable to translate the map, they go to nearby Port Royal for a translator. There, they learn that a criminal being sold into slavery, a con man and thief named William Shaw, is fluent in Latin. After threatening a man determined to outbid her, Morgan wins the auction. When she is recognized from her wanted poster and barely escapes with her crew and Shaw, corrupt Governor Ainslee vows to find her after learning of the treasure's existence. He enlists the help of John Reed, an infamous chronicler of pirates and crew member of the Morning Star.

The crew finds Mordechai in Spittlefield Harbor. Before they can learn where the second piece is, Dawg and his crew raid the harbor. A fight ensues, during which Mordechai is killed and Morgan is shot, while Shaw secretly finds the piece and keeps it to himself. After they escape on the Morning Star, Morgan collapses from her wound, but Shaw uses his limited medical knowledge to save her. The two start a romance. Morgan figures out that the words on the two map pieces, when read backwards, spell out half the coordinates to the island.

Dawg pursues the Morning Star in his own ship, the Reaper. Morgan directs hers toward a coral reef and a gale to shake her pursuers off. Shaw manages to piece together the location of Cutthroat Island with his and Morgan's piece but is caught and thrown in the brig. During the storm, Reed secretly sends a carrier pigeon revealing their location to Ainslee. Meanwhile, the majority of the crew, led by the treacherous boatswain Scully, mutinies and maroons Morgan and those loyal to her in a boat. The tide takes them straight to Cutthroat Island.

As Morgan goes after the treasure, Shaw escapes and steals the last map piece from Dawg. Shaw falls into quicksand and Morgan, realizing he has the piece, frees him. Together they find the treasure, only for it to be stolen by Dawg, forcing them to jump off a cliff into the tide. After regaining consciousness, Shaw finds Reed, who leads him into a trap set by Dawg, Ainslee, and Scully, who have joined forces and intend to split the treasure. As Shaw is captured and they make their way out to sea with the gold, Morgan sneaks aboard the Morning Star and retakes it from Scully and the mutineers.

The crew then tries to sneak attack the Reaper, but Dawg counterattacks. A sea fight ensues, during which Shaw escapes and Ainslee, his men, and Reed are killed by cannon fire. Morgan boards the Reaper and blows out the ship's bottom. She then duels Dawg while Shaw gets trapped below in rapidly rising water with the treasure. Morgan kills Dawg with a cannon and saves Shaw, forced to abandon the treasure to escape the sinking ship.

Morgan had attached a marker barrel to the treasure beforehand, allowing them to retrieve it, and the newly rich crew sets sail for Madagascar.