To control the oceans, Lord Cutler Beckett executes anyone associated with piracy in Port Royal and orders Davy Jones to destroy all pirate ships. Condemned prisoners sing "Hoist the Colours" to compel the nine Pirate Lords to convene at Shipwreck Cove to hold the Brethren Court. Because Pirate Lord Jack Sparrow never named a successor before being dragged to Davy Jones' Locker, Hector Barbossa, Will Turner, Elizabeth Swann, Tia Dalma, and the surviving crew of the Black Pearl plot to rescue Jack. In Singapore, the crew meet Pirate Lord Sao Feng, who owns navigational charts to the Locker. They are then attacked by the East India Trading Company. During the battle, Will secretly promises to give Jack to Feng in return for the Pearl, intending to use it to rescue his father "Bootstrap Bill" Turner from the Flying Dutchman.

The crew rescue Jack and recover the Pearl. As they depart, they encounter boats of dead souls, including Elizabeth's father Governor Swann, executed by Beckett. Tia Dalma reveals that the goddess Calypso charged Davy Jones with guiding the souls of those who died at sea to the next world; every ten years he could come ashore to be with the woman he loved, but Jones corrupted his purpose and was cursed to become a monster. Governor Swann reveals that whoever kills Jones by stabbing his disembodied heart must become the Dutchman's captain.

Returning to the living world, the Pearl stops at an island for fresh water, but are attacked by Sao Feng and Beckett's men. As Jack secretly negotiates his freedom with Beckett, Elizabeth is handed over to Feng, who believes she is Calypso, while the rest of the crew make for Shipwreck Cove aboard the Pearl. Jack throws Will off the ship as part of a 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; Feng plans to release her to defeat Beckett. Feng is fatally wounded in an attack by Jones, appointing Elizabeth his successor as Pirate Lord before dying. Elizabeth and the crew are locked in the brig of the Dutchman, where she finds Bootstrap Bill losing himself to the Dutchman's curse. Admiral James Norrington frees Elizabeth and her crew from the Dutchman, but is killed by a crazed Bootstrap Bill.

Will is rescued by Beckett and informs Jones of Jack's escape from the Locker, learning in the process that Jones enabled the first Court to imprison Calypso, revealed to be Tia Dalma. Meanwhile, the Pearl arrives at Shipwreck Cove, where Barbossa attempts to persuade the Brethren Court to release Calypso while Elizabeth demands they fight back against Beckett. Jack's father, Captain Teague, informs the Court that only an elected Pirate King can declare war. To avoid a stalemate, Jack votes for Elizabeth, making her King. Elizabeth, Jack, Barbossa, Beckett, Jones, and Will parley, trading Will for Jack. Barbossa frees Calypso, but when Will reveals Jones' betrayal to her; refusing to help either side, Calypso vanishes and summons a maelstrom.