The story unfolds in Jamaica in 1668, where the clever pirate Morgan Adams (Geena Davis) manages to outsmart a bounty hunter attempting to capture her. As she embarks on a mission to locate her uncle, Dawg Brown (Frank Langella), who has taken her father, Black Harry (Harris Yulin), hostage, the plot thickens. Harry possesses one of three crucial pieces of a treasure map leading to an immense fortune buried on the remote Cutthroat Island. Dawg has another piece, stolen from a deceased brother, while their elusive sibling, Mordachai (George Murcell), holds the third.
Dawg tries to coerce Harry into revealing the map's location, but Harry refuses and escapes, albeit mortally wounded with Morgan’s assistance. Before his passing, he discloses the startling secret of the map's whereabouts—hidden within his own scalp. After a daring act of scalping her deceased father for the precious map piece, Morgan takes charge of her father’s ship, the Morning Star, and sets sail in search of the treasure.
However, complications arise when they discover that the map's instructions are written in Latin, a language none of the crew can decipher. Their quest leads them to Port Royal, where they find a shrewd con artist named William Shaw (Matthew Modine), who is fluent in Latin and up for auction. After a confrontation with another buyer, Morgan successfully secures Shaw. Yet, her infamy catches up with her as she must flee the town with her crew amid chaos.
The corrupt governor, Ainslee (Patrick Malahide), intent on capturing Morgan or striking a deal for half her riches, recruits chronicler John Reed (Maury Chaykin) to aid in his efforts. Their next destination is Mordachai’s hideout in Spittlefield Harbor, where they seek the second piece of the treasure map. However, a confrontation with Dawg results in a fierce battle, leading to Mordachai’s death and Morgan sustaining a gunshot wound. During the chaos, Shaw secretly acquires the map piece.
As they attempt to escape on the Morning Star, Morgan’s injury renders her weak, but Shaw, claiming to be a doctor, tends to her wounds. Their bond grows as they decipher the map's wording, which reveals half of the island's location when read backward. Their journey is fraught with danger, including an impending attack from Dawg’s ship, the Reaper. In a moment of desperation, Morgan skillfully navigates towards coral reefs amid a violent storm.
Shaw’s attempts to piece together the map lead him to imprisonment in the brig, while Reed betrays them by sending a pigeon to Ainslee, revealing their position. Meanwhile, dissatisfaction brews among the crew, led by the traitorous Scully (Jimmie F. Skaggs), resulting in a mutiny against Morgan. Ironically, the wreckage of their boat washes them directly to Cutthroat Island.
In a surprising twist, Morgan pursues the treasure, only to find Shaw, who has escaped the storm but becomes trapped in quicksand while possessing the map piece. Together, they manage to discover the long-lost gold. However, in a climactic turn of events, Dawg snatches the treasure, forcing them to leap off a cliff into the ocean.
Recovering from their tumble into the waves, Shaw inadvertently leads himself into a trap laid by Dawg, Ainslee, and the mutineers. As they set sail with their stolen riches, Morgan, undeterred, commandeers the Morning Star back from the treacherous crew. What follows is an epic naval confrontation with the Reaper; during the chaos, Ainslee meets his end in a cannon blast.
In a gripping climax, Morgan faces off against Dawg and, with ingenuity, dispatches him using cannon fire while Shaw struggles in the rising waters with the treasure. Though they must forsake the gold to escape the crumbling ship, fortune smiles upon them as Morgan employs a clever stratagem to recover their newfound wealth. The reinvigorated crew then sets their sights on their next adventure in Madagascar, ready to embrace the thrills that await them.
