The Longitude Chronometer, a device that will change the world, is stolen from HMS Petrel by pirates working for the legendary but supposedly long dead Edward Teach - better known as Blackbeard. On board the Petrel is Tom Lowe, an English spy working undercover as ship's surgeon. Lowe's mission is to prevent the Chronometer from falling into the hands of pirates - and if the opportunity should arise, to assassinate Blackbeard.
Blackbeard's plans are complicated when a popular Pirate Captain comes to town and violently disagrees with his grand design. For his master plan to survive, Blackbeard must weigh the risks of ridding himself of a dangerous old friend. Meanwhile, trying to gain insight into the Commodore's mysterious endgame, Tom Lowe finds himself an unlikely instrument of Blackbeard's will.
When Kate is captured on a trading voyage, Blackbeard and Lowe must work together in order to rescue her before she reveals the island's whereabouts to William Jagger. In the process, Lowe discovers that Blackbeard has an ulterior, deeply personal motive for keeping him on Santa Compana.
Having learned of Blackbeard's plans to attack innocent civilians in Jamaica, Lowe devises a way to report back to his spymaster, William Jagger. But having done so, Lowe discovers that Jagger might be an even greater madman than the Commodore. The time has come to make a choice between two evils. Which way will he jump?
Lowe plots to kidnap Blackbeard and deliver him to the English authorities, believing this to be the only way to save the people of Santa Compana from the mad wrath of William Jagger. Meanwhile, Jagger visits an insane asylum, believing a patient there will be the key to finally defeating Blackbeard.
Balfour overhears Lowe confess to Kate of being an English spy sent to kill Blackbeard and he tells Selima, who sends pirates to find Lowe. Antoinette's torture continues at the hands of Jagger, now using Lowe's sketchbook as evidence that Edward "Blackbeard" Teach is alive. To comfort herself, she recites an encrypted rhyme. Jagger cracks the code - the chronometer Blackbeard sold to the Spanish will lead the fleet to a surprise attack from Blackbeard himself, the only one who knows where the Spaniards, and their treasure, will be.
With few alllies left in Santa Compana, things take a turn for the worse for Lowe when Nenna's plans for escape puts him in her deadly crosshairs. Meanwhile, Balfour makes an unexpected alliance that could cost both him and Lowe their lives.
Fire rains down on Santa Campana as Blackbeard risks all against William Jagger's maniacal attack. Lowe must choose between saving the people he loves, the man he admires and the legacy Edward Teach has built.