Season 2

Complete listed story — includes the ending

1. IX.

The Walrus crew is stranded on the beach with an army of Spanish soldiers standing between them and the gold on the Urca de Lima. When going before his former crew to face judgment for his crimes, Flint devises a plan for survival to sneak aboard the warship and take out the watchmen. Thinking he means to escape, Silver volunteers to go on the mission. Meanwhile, Eleanor struggles to maintain her hold on Nassau as a new threat arrives; the murderous pirate Ned Low and his equally violent crew from his ship, Fancy. Also, Vane has a new position at the fort on New Providence, while Jack is reduced to being labelled a "crew-killer" and endures daily beatings.

2. X.

A member of the Walrus crew unexpectedly returns, but finds himself cruelly tethered down on a beach. Flint, still stuck in the bowels of the ship, sets his plan in motion to become a captain in two days' time by offering advice to Dufresne on a certain route to navigate the galleon through. Meanwhile, Silver tries to make himself indispensable to his crewmates by reading them gossip that the quiet cook Randall witnesses daily aboard the ship. Meeks asks Eleanor to dispose of his captain, Ned Low since his unquenchable thirst for power is causing the crew to be reckless. After Jack learns about the intimate encounter between Max and Anne, he accepts it and later proposes his next money-making scheme with them.

3. XI.

When Flint returns to Nassau to seek help retrieving the gold, he encounters a problem when he learns that Hornigold no longer commands the fort on the island, and anchors the Spanish warship in the bay directly in line with it. No longer considered a "crew-killer," Rackham's reputation is restored, but he is worried that Anne is being taken advantage of by Max, driving a wedge between them. Later, Vane is confronted by Ned Low, who learns of his intimate relationship with Eleanor and threatens her well-being after being provoked. This causes Vane to take action and devise a plan to board Low's ship, kill him and steal his crew, but in the process, Vane discovers Low is carrying 'precious cargo' in the brig.

4. XII.

Wanting to remove Vane from the fort, Flint sends a messenger to him issuing a warning. Eleanor tries to put an end to Flint's plan to demolish the fort, giving him an ultimatum; however, the final decision rests in his hands only. Meanwhile, Vane learns that Low's special cargo is Abigail Ashe, daughter of Carolina's governor, and plots to ransom her off. Rackham admires what Max can do with the help of one of her ladies in order to gain him a ship and crew, making him a captain again. Silver, while ensuring his portion of the gold, makes use of his time on the island by playing to the locals with gossip, but in doing so, he is reunited with an old crew member from the Walrus who is badly malnourished.

5. XIII.

Flint begins the bombardment of Vane's fort in earnest. After destroying a portion of the wall, Flint and Hornigold stage their crews on the beach, arming them to retake the fort. During the bombardment, it is shown through a series of flashbacks that not only had Flint wholly committed himself to Hamilton's plan to retake Nassau and pardon the pirates, but had also begun an affair with him. While seeking support from his commander, Flint is confronted by him and Lord Hamilton, who strip Flint of his rank and expel him from the Royal Navy. They give Flint and Ms. Hamilton until nightfall to flee London while committing Mr. Hamilton to a mental hospital. In the present, Ms. Hamilton, now Ms. Barlow, rides into town to try to avert the bloodshed of the coming battle. She finally gets Flint alone and tells him of Abigail Ashe, the daughter of a once-trusted friend. She says they should trade her for safety in the Colonies, thus finally making possible Mr. Hamilton's plan. She leaves Flint a copy of "Marcus Aurelius," which has a dedication to Flint by Mr. Hamilton. After she departs, Vane bursts into the room with a dagger.

6. XIV.

To spare Flint exposure to his crew, Billy Bones decides to remain silent and not go ahead with his plans for revenge. However, he later states that he was captured and interrogated by the Royal Navy, and was given the option to denounce Flint for a pardon. Flint retracts his promises to capture the fort, kill Vane, and raid the Spanish gold so that he can regain a legitimate reputation by following Eleanor and Miranda's plan to return the daughter of the governor of Carolina. Jack Rackham finally takes on his maiden voyage as a captain, but it takes a turn for the worse when his ship is boarded by rival pirates, who have a stronger crew and heavier weaponry. They give Rackham the option of a sharing term, and due to the pitiful nature of it, Rackham decides to risk a confrontation with the rival captain.

7. XV.

The pirates prepare to take a vote on whether Flint or Hornigold should become captain, causing Flint's plans to take a halt. Billy secretly meets with Dufresne and declares his plan to gather at least ten men that oppose Flint, to capture him and surrender him to the British authorities, so that they may all receive full pardons for their piracy. Two scouts tasked with watching the Urca gold return to report that the Spanish crew died from a tropical disease, leaving the gold unprotected. John, intercepting them, convinces them to tell Flint that the gold is now gone so that John can organize a secret expedition with Max to gather it without any issues or opposition. As part of the plan for pardons for Flint and Miranda, Eleanor betrays Vane by helping Abigail to escape.

8. XVI.

Billy's trap to eliminate the traitors of the pirate crew succeeds, and Flint ends up winning against Hornigold in the election for the captaincy. After the election and its results against him, Hornigold departs from Nassau. Flint also leaves Nassau, but instead sails to Carolina to meet with the governor there in regards to his daughter; Carolina is a place where pirates are believed to be most evil and the attitude towards them is extremely hostile. John Silver discusses the plan for the retrieval of the unguarded Spanish gold with Jack Rackham and his crew. Mrs. Mapleton reveals to Eleanor the plan to retrieve the gold, and they both agree that the plan goes against the dream that they share for Nassau, to transform the pirate town into a legitimate community.

9. XVII.

While Flint's ship waits in the Charles Town harbour, Vane overtakes the ship. However, Billy remains faithful to Flint's cause, and Silver remains on board, hiding with a few of the survivors. In Nassau, the remaining traitors that were not captured join forces to take Eleanor as hostage. They deliver her to the Royal Navy so that they can receive their ten full pardons for their actions as pirates. Flint prepares to accept the conditions of Peter Ashe, the Carolina governor, which are to expose his whole story to London and allow an inspection of the pirate port of Nassau. However, Miranda comes to the realization that it was Peter who betrayed them so many years ago. She retracts her deal with the governor and demands that Peter be hanged for his betrayal, leading to Peter's guards capturing Flint and killing Miranda. Flint's trial is later announced. Upon hearing the news of Flint's upcoming trial, Vane suggests an alliance with Billy to save Flint.

10. XVIII.

In Charles Town, the day of Captain Flint's trial comes. Lord Ashe offers him a chance to avoid humiliation, but Flint declines, still bitter at Ashe for Mrs. Barlow's death. However, help for Flint arrives in the unlikeliest form: Charles Vane. Vane's men launch their attack on the city using its own cannons, and Flint and Vane fight their way out, with Flint murdering Ashe en route. They reach the ship to find Flint's crew have regained leadership, but Flint orders Vane's crew be released - realizing pirates have to unite against the rest of the world. Silver, after being tortured, is forced to have his leg amputated. When he finally awakens, he reveals that the spy they hired to watch the Spanish soldiers sold the location to Jack, but he leaves out his own part in the exchange. The ending scene shows Max celebrating Jack's success at bringing the treasure back to Nassau.