Lord Cutler Beckett begins executing anyone associated with piracy and commands Davy Jones to destroy all pirate ships. To confront Beckett's assault, the nine pirate lords making up the Brethren Court have been summoned to convene on Shipwreck Island. However, Captain Jack Sparrow, pirate lord of the Caribbean, never appointed his successor, and therefore must be present. Captain Barbossa leads Will , Elizabeth, Tia Dalma and the Black Pearl crew to rescue Jack. Sao Feng, pirate lord of Singapore, possesses a map to World's End, the gateway to Davy Jones' Locker. Elizabeth and Barbossa attempt to bargain with Feng for the map and a ship, but Feng is furious that Will already attempted to steal it. The British Royal Navy , acting under orders from Beckett, suddenly attack Feng's bathhouse. During the ensuing chaos, Will strikes a bargain with Feng for the Black Pearl in exchange for Sparrow, whom Feng wants to turn over to Beckett, presumably in exchange for immunity from Davy Jones' attacks on pirates. Will wants the Black Pearl to rescue his father from the Flying Dutchman .
The crew journey through a frozen sea and sail over an enormous waterfall into the Locker. Aboard the Pearl , Sparrow is suffering hallucinations about an entire crew comprised of himself. The Pearl is dragged to an ocean shore by crab-like creatures, and Jack is reunited with his old shipmates, though he is initially reluctant to rejoin a crew that have attempted to kill and mutinied against him. As the Black Pearl the crew seeks an escape route, they see dead souls floating under the water. Tia Dalma says that Davy Jones was appointed by his lover, Calypso, goddess of the sea, to ferry the dead to the next world. In return, Jones was allowed to step upon land for one day every ten years to be with his love, but when she failed to meet him, the scorned captain abandoned his duty and transformed into a monster. Elizabeth sees her father, Governor Weatherby Swann's soul pass by in a boat; he was murdered by Beckett. A distraught Elizabeth vows revenge.
The Black Pearl remains trapped in the Locker until Sparrow deciphers the map, realizing the ship must be capsized to return to the living world. They overturn the ship, and at sunset, upturn back into the living world. Upon their return, Sao Feng attacks, revealing his agreement with Will. But he betrays Will, having made a deal with Cutler Beckett to hand over the crew and keep the Black Pearl . Onboard ‘'Endeavor'', Sparrow refuses to divulge to Beckett where the Brethren Court will convene. Beckett double-crosses Feng by keeping the Black Pearl for his armada, and in turn Feng gives Sparrow the ship back, while taking Elizabeth, whom he believes is Calypso. Aboard his warship, the Empress , Feng tells Elizabeth that it was the first Brethren Court who trapped Calypso into human form so they could control the seas. Feng is mortally wounded when Davy Jones attacks his ship. Before dying, he appoints Elizabeth his heir, making her captain and the pirate lord of Singapore. She and the crew are imprisoned in Flying Dutchman' s brig. Also aboard is Admiral James Norrington, who betrays Beckett and frees Elizabeth and her crew who escape back to their ship, although Norrington is killed when he is discovered by Bootstrap Bill.
Will leaves a trail of corpses for Beckett's ship to follow. Sparrow catches him and tosses him overboard, but he first gives him his magical compass, apparently intending for Beckett to find them. Will is picked up by Beckett's ship, and it is revealed that it was Davy Jones who masterminded Calypso's imprisonment by the pirate lords. At Shipwreck Island, the nine pirate lords disagree over freeing Calypso. Elizabeth arrives and is elected "Pirate King" after Sparrow's vote breaks a stalemate. She orders the pirates to fight Beckett. During parlay with Beckett and Jones, Elizabeth and Barbossa swap Sparrow for Will. Barbossa tricked the other pirate lords into giving him their insignias, which he needs to free Calypso, who is Tia Dalma. When Barbossa releases her in a ritual, her fury over Jones' betrayal unleashes a violent maelstrom just as the Navy's massive fleet appears on the horizon. During the battle, Sparrow escapes the Flying Dutchman with the Dead Man's Chest. As the Black Pearl and the Flying Dutchman face off near the centre of a massive whirlpool, Will proposes to Elizabeth. They insist that Barbossa marry them as they are fighting Jones' crew and the Royal Navy. When Davy Jones mortally wounds Will aboard his ship, Bootstrap Bill attacks Jones. Jack, who wanted the heart for his own immortality, places a knife in Will's hand and helps him stab Jones' heart, killing Jones and making Will the Flying Dutchman' s captain. The crew cut out Will's heart and place it into the Dead Man's Chest : the crewmen regain their humanity, and Will and Sparrow captain the Flying Dutchman and the Black Pearl respectively to destroy Beckett's ship, the Endeavor, forcing the enemy fleet to retreat.
Although Will has been saved and the Dutchman crew has regained their humanity, he must now spend the next ten years at sea. He and Elizabeth have one day together and consummate their marriage on an island before Will must leave for his new life. Will gives Elizabeth the ‘'Dead Man's Chest'' for safekeeping. Shortly after, Barbossa again commandeers the Black Pearl , stranding Jack and Gibbs in Tortuga. Having anticipated Barbossa's deception, however, Sparrow has already removed the map's middle that leads to the Fountain of Youth. In a post-credits scene set ten years later, Will reunites with Elizabeth and their son.