The film begins with Lord Cutler Beckett unmercifully executing mass amounts of people who are associated with piracy. Among them is an innocent looking young boy who starts singing a pirate song, Hoist the Colours. This song continues to be sung by the group who is waiting to be executed and it leads on to Elizabeth Swann, who is rowing a small sampan in Singapore. She arrives on shore with Captain Barbossa and they enter the bath house of Chinese pirate Sao Feng. Outside, Tia Dalma is disguised as a common hawker, and the rest of the crew break into the bath house for backup in case a fight breaks out.Inside, Captain Barbossa and Elizabeth reveal that they are here to ask for a ship and crew so they can rescue Jack Sparrow, who is trapped in Davy Jones' Locker. Sao Feng laughs as this request, claiming to be mortal enemies with Jack Sparrow, and revealing the coincidence that a thief had come to steal his navigational charts earlier that day. Will Turner, the thief, is pulled out of a tub of water and both Elizabeth and Barbossa look surprised, as they never expected Will to get caught. Sao Feng asks if the thief is part of theirs, and both of them deny it. But Elizabeth cries out just as Sao is about to stab Will. Sao Feng stops and spots a man with a fake dragon tattoo. Assuming that he is part of Barbossa's crew, Sao Feng's men pull out their swords, ready to fight and Barbossa and Elizabeth. Will points out the fake tattoo man isn't part of either party and suddenly, soldiers of the East India Trading Company burst in through the door firing their guns. A fight between the pirates and the Company ensue. Sao Feng and Will fight but negotiate a deal and Sao Feng offers them a junk and crew. Mr. Mercer, Beckett's right hand man in hiding overhears this but does not kill either of them.
Barbossa, Elizabeth, Will and the crew journey through a frozen ocean, with the help of Sao Feng's maps which Will stole after the fight. Tia Dalma explains that she couldn't revive Captain Jack Sparrow the same way as Barbossa as Barbossa was only killed, and his soul was taken to the land of the dead. As for Jack, he was taken both body and soul to Davy Jones' Locker. They continue sailing until Will spots at the horizon an enormous waterfall, which is the world's edge where all the sea water pours over, and orders the crew to turn the ship around. However, Barbossa dismisses that order and shouts for the crew to let the ship be. They fall down the waterfall and into Davy Jones' Locker.
While imprisoned there, Jack Sparrow is confronted with the many facets of his character before jumping off his marooned Black Pearl. All around the ship is plain desert and with the help of some crabs, the Black Pearl is able to be dragged towards a beach. At that moment, the crew from the junk arrive and see the ship and Jack himself. They greet him warm heartedly, but Jack retorts that why should he sail with them, since four of them had tried to kill him, and one of them succeeded. Will turns around to see Elizabeth looking guilty as ever.
Despite their mutual animosity and distrust, Sparrow and Barbossa form an alliance when they discover Cutler Beckett possesses the heart of Davy Jones, has begun purging piracy with the commanded assistance of Davy Jones and the Flying Dutchman ship. The world's pirates must gather for a meeting of the brotherhood known as the Brethren Court, consisting of nine pirate lords, and they should hurry, because the pirate song has already been sung.
During a squabble between Sparrow and Barbossa on board the Black Pearl, Sao Feng and his men appear claiming the ship and names Will as captain. Everyone is taken by surprise, especially Elizabeth. Barbossa tries to negotiate a deal, claiming he has Calypso, goddess of the sea, in her human form. Sao Feng looks at Elizabeth and captures her to his ship, the Empress. That evening Sao Feng pampers the captured Elizabeth and calls her Calypso. The Empress is suddenly attacked by the Flying Dutchman and Sao Feng is killed. Elizabeth is chosen by him to be the new captain of the Empress, due to his belief that she is Calypso, despite the revelation that Tia Dalma is. The Empress crew and Elizabeth is then held prisoner in the Flying Dutchman, controlled by Lord Beckett.
On board the Flying Dutchman, Elizabeth meets Will's father, Bootstrap Bill who appears to have amnesia. James Norrington, the East India Trading Company commander of the Flying Dutchman frees the Empress crew and Elizabeth. Bootstrap Bill realizes this, alarms others and then kills James Norrington.
At the Brethren Court, eight of the nine pirate lords discuss the threat of Beckett and the release of Calypso from her imprisoned human form. Expecting Sao Feng to show up and reach a decision, they see Elizabeth instead. Every pirate argues over the matters at hand because Elizabeth has proposed for war. However, Barbossa claims that only the king can make such a decision. After Captain Teague prooves it to be correct, Jack demands that they vote for a king. Since every pirate lord only has one vote, and that they would only vote for themselves, everyone is taken by awe when Jack votes for Elizabeth instead of himself, making her the Pirate King of the Brethren. Against Barbossa's persuasion, Elizabeth orders the pirates to fight against Beckett and leave Calypso be.
As all the pirates get ready to fight they see the horizon filled with Lord Beckett's massive fleet and are dumbstruck. A parley is called, and in attendance are Will Turner, Lord Beckett, and Davy Jones on side, then Captain Barbossa, Elizabeth, and Captain Jack on the other side. A deal is made to exchange Will for Jack, which Barbossa vehemently disagrees with, slicing off Jack's piece of eight and taking it.
Upon their return to the ship, Barbossa frees Tia Dalma/Calypso and asks her to help in the battle between pirates, Davy Jones, the Royal Navy, and the East India Trading Company. In this climactic battle in a maelstrom, Elizabeth and Will are joined in matrimony by Captain Barbossa whilst fighting the crew of the Flying Dutchman. Soon after Davy Jones stabs Will in the heart, but Jack takes Davy Jones' heart and lifts Will's hand and stabs it, killing Davy Jones.
He who kills the captain of the Flying Dutchman must replace the captain for eternity. Therefore Will is now the captain of the Flying Dutchman. Elizabeth is heartbroken, thinking Will is dead, but as the Flying Dutchman emerges from within the sea, Will is alive and the crew has returned to normal. The pirates of the Black Pearl and the Flying Dutchman then turn to face Cutler Beckett, and sink him and his ship to the depths.
The pirates emerge victorious, but learn that the Flying Dutchman must stay in the undersea-world and can only come to shore for one day, every ten years. Until then, Will must ferry the dead for ten years, and will be trapped on the ship if his love is not true. Will and Elizabeth spend their "last day" together on a beach and she promises she will wait for him and keep his heart safe. Jack embarks on a quest to find the fountain of youth.
After the credits, in a scene captioned "Ten Years Later," a young boy approximately ten years of age is seen singing "Hoist the Colours" as Elizabeth walks behind him. It is implied that this is the child of Will and Elizabeth. The sun sets followed by a green flash and Will, on the mast of The Dutchman, sails towards the shore.
