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 unhappyly 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 Blackbeard receives word that Kate has been captured by the English, he sets out to rescue her before Jagger tortures the location of Santa Compana out of her. However, Tom and James have their doubts that Blackbeard intends to keep her alive and Tom goes with Blackbeard to guarantee her safety.

James asks Tom to help him overcome his opium addiction and regain the partial use of his legs. However, Blackbeard has other plans for Tom, sending him to steal from a Cuban governor so that he can finance the army he needs for the next stage of his master plan. Meanwhile, Jagger turns to an unexpected resource to find Santa Campana.

Tom tricks Blackbeard into letting him return to Jamaica. However, when Jagger demands Santa Campana's location, Tom realizes that the governor-general willhug the guilty and innocent alike and has second thoughts. Meanwhile, Rose blackmails Nenna, who seeks to buy a plantation for herself. And Blackbeard encourages Selima to leave the manor in preparation of her taking his place if he dies.

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.

After the revelation that Tom is a spy, Nelly approaches him and asks for his help dealing with Nenna. Tom agrees to do so, but soon finds himself at risk of his life. Meanwhile, James reveals to Kate what kind of man he really is.

Under pressure from a mysterious, powerful warlord, Blackbeard dispatches Rider, Nenna, and Tom Lowe to carry out a daring raid on a Spanish stronghold. But Lowe is far from welcome on this mission.

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.