This epic story begins in 1708 Plymouth, England. 16-year-old Mary Read, running away from home and a brothel her mother was forcing her to work as a maid, disguises herself as a boy and boards a man-o'-war off to Flanders to fight the French where she becomes famous for her bravery-- and even more famous when the world discovers the brave soldier is a woman. Her commanding general marries her on the battlefield to her Lieutenant, Max Sturdevant.
Meanwhile, back in the colonies, 16-year-old Anne Cormac is sitting down at a formal dinner with her parents and guests-- including the Governor of the Carolinas-- when Ned Teach-- Black Beard-- interrupts the festivities with guns blazing and gunners matches under his hat set afire. Everyone cowers except Anne who stands up to him and puts him in his place with a few well-chosen words and a well-thrown knife. He's there to get the governor's blessing to sell his contraband at an auction. The governor, fearing for his life, agrees. Meeting Black Beard excites Anne and within a very short time marries James Bonny who takes her to Nassau which, at that time, is a veritable pirate playground. It's here where she dumps her husband and takes up with pirate Calico Jack Rackham and becomes close friends with the very gay and black pirate Henri Duplaissez.
The next time we see Mary Read is on board the pirate vessel The Royal Fortune. Disguised as a man-- her husband now dead-- Mary has taken up pirating with Black Bart.
Anne Bonny has taken up with Tombay, an African she's fallen in love with and had a baby. Returning from fishing, she stumbles upon Spaniards killing her husband and baby. A swordfight ensues and she kills them.
Later, in Nassau, Anne, now living with Rackham, finally meets Mary in a tavern. Mary, still disguised as a man and having achieved the rank of quartermaster, is surprised to see Anne living life like a woman without a care in the world. Weeks later after a fight with Rackham, Anne kisses Mary and Mary responds. When Anne feels Mary's breasts, she stops short and can't believe that Mary isn't a man. Mary asks her to swear secrecy. Unfortunately, Rackham finds them together, and still drunk, tries to kill Mary in a sword fight-- until her vest flies open revealing her breasts. Stunned, he too is sworn to secrecy.
Anne's husband James Bonny reports her to the newly arrived Nassau governor Woods Rogers for having a scandalous affair with Rackham. The pirates are rounded up and thrown in jail. Anne is tied to a stake, stripped of her blouse and whipped by a cat of nine tails. Henri carries out an elaborate and funny escape plan which has them dressing up in drag to seduce the guards. It works and everyone skips Nassau in the night aboard a small sloop.
They resume piracy and live life on the run. Mary falls in love with Tobias Sampson, a carpenter who opted to join up with them after they scuttled his English ship. Mary still insists on keeping her identity a secret even after they are married. Unfortunately, a short while later a pirate tries to kill Tobias because he thinks Mary's husband is a sodomite. Mary jumps in on her husband's behalf and kills the offended pirate.
Months later Mary, now pregnant, and Anne must depend on themselves to fight the British who have swooped down on them unexpectedly. Rackham and most of the other pirates are drunk and unable to offer any help.
Imprisoned, they are put on trial in Spanish Town by Governor Lawes, a hard-ass with little sympathy for pirates-- especially women pirates. Tobias refuses to confess and Lawes tortures him to death. Rackham is hanged and put in an iron cage overlooking the harbor for seagulls to feast upon and as a warning to others contemplating piracy. Mary gives birth in prison to a baby boy. The film ends with Mary dying in Anne's arms while in prison.