To control the oceans, Lord Cutler Beckett executes anyone associated with piracy by ordering Davy Jones to destroy all pirate ships in the seas. Condemned prisoners sing "Hoist the Colours" to compel the nine Pirate Lords to convene at Shipwreck Cove to hold the Brethren Court. Because Captain Jack Sparrow, one of the Pirate Lords, never named a successor, before being killed, Captain Barbossa, along with Will Turner, Elizabeth Swann, Tia Dalma, and the crew of the Black Pearl, plot to rescue Jack from Davy Jones's Locker. Travelling to Singapore, the crew meet Captain Sao Feng who owns navigational charts to the Locker and quickly gains an unpredictable interest in Elizabeth. Beckett's soldiers invade, but the crew escape. Feng and Turner make a deal to give Jack to Feng, so he in turn can use the Pearl to rescue his father Bootstrap Bill from the Flying Dutchman. The crew travels to the locker and rescues the marooned Jack. They find themselves trapped, encountering dead souls, including Elizabeth's father Governor Swann. They learn the Dutchman must have a captain.
Returning to the living world, the Pearl is attacked by Sao Feng and Beckett's men. Through a complex series of deals, Elizabeth is handed over to Feng who believes she is the goddess Calypso, while the rest of the crew make for Shipwreck Cove aboard the Pearl, though Jack later throws Will off the ship as part of the plan to seize control of the Dutchman. Sao Feng tells Elizabeth that the first Brethren Court bound Calypso in human form after she betrayed her lover, Davy Jones. He plans to release her to defeat Beckett. Davy Jones attacks Feng's ship, but Feng appoints Elizabeth his successor as Pirate Lord before dying. Admiral Norrington frees Elizabeth and her new crew from the Dutchman, but is killed by a crazed Bootstrap Bill.
The Black Pearl arrives at Shipwreck Cove where Barbossa attempts to persuade the Brethren Court to release Calypso. Jack's father Captain Teague and Keeper of the Pirate Code, informs the Court that only an elected Pirate King can decide. A vote is taken. To avoid a stalemate, Jack casts his vote for Elizabeth, making her King. Davy Jones visits Tia Dalma in the Pearl's brig, revealing she is Calypso, and they promise to be together again.
The Brethren Court and Beckett's fleets emerge for war. On a sandbank, Elizabeth, Jack, Barbossa, Beckett, Jones, and Will parley, trading Will for Jack, and Barbossa steals Jack's piece of eight, all of which are owned by the Pirate Lords and required to free Calypso. Barbossa frees Calypso, but when Will reveals it was Jones who made it possible for the first Court to imprison her, Calypso vanishes and summons an enormous maelstrom.
The Pearl and the Dutchman battle in the maelstrom. Elizabeth and Will are wed by Barbossa before swinging over to the Dutchman to aid Jack. On board the Dutchman, Jones and Jack engage in a duel, with Jones gaining the upper hand. Jones stabs Will with a sword, but Jack and Elizabeth have Will stab Jones' heart. Jones dies, and falls in the maelstrom, free for all eternity. Will succumbs to his injuries. Jack and Elizabeth escape the Dutchman as it is sucked into the maelstrom. As Beckett's ship, the Endeavour, approaches to destroy the Pearl, the Dutchman rises, now captained by Will, and the crew free of Jones' curse. Together, the two pirate ships destroy the Endeavour, with a stunned Beckett going down with the ship while his navy retreats, demoralized by the loss of both the Endeavor and their commander in Beckett. With Will now bound to escort souls lost at sea to the next world for ten years, Will and Elizabeth consummate their marriage before he departs on the Dutchman.
Jack and Joshamee Gibbs discover Barbossa has stolen the Black Pearl again, but Jack planned ahead and cut out Sao Feng's navigational charts, departing from Tortuga alone to track down the mythical Fountain of Youth to become immortal.
In a post-credits scene, set ten years later, Elizabeth and her son, Henry, watch from a sea cliff as Will returns aboard the Dutchman.
Who falls in the maelstrom?
Jones