Some time after the events of the previous film, Lord Cutler Beckett, head of the East India Trading Company, arrests Will Turner and his fiance Elizabeth Swann for their role in helping Captain Jack Sparrow escape his execution. Elsewhere, Jack, now captain of the Black Pearl, escapes from a Turkish prison with a drawing of a key, and convinces his crew to search for the key in question. When he tries to use his compass to pick a heading however, the compass refuses to work.
In Port Royal, Beckett has Will brought to his office and makes him an offer; if Will can find Jack and convince him to part with his compass, he and Elizabeth will be set free, otherwise they’ll be hanged. Beckett reveals that he is prepared to offer a letter of marque and a full pardon to Jack, clearing his name in exchange for his service and the compass.
Aboard the Black Pearl, Jack goes below decks for some rum, where he encounters “Bootstrap Bill” Turner, Will’s father and a former crew member of Jack’s from before Barbossa’s mutiny. Bootstrap tells Jack that as punishment for his opposition to the mutiny, Barbossa had him tied to a cannon and dropped into the ocean, a Fate Worse than Death for an immortal pirate. To escape this, Bootstrap entered into the service of Davy Jones, another supernaturally-enhanced pirate and the captain of the Flying Dutchman. Bootstrap reminds Jack that he made a deal with Jones as well; in exchange for Jones raising the Pearl from the depths of the ocean, Jack’s soul would belong to Jones thirteen years later. Bootstrap warns Jack that the Kraken - another servant of Jones - will be hunting him from now on, supernaturally marking his hand with a black spot as a permanent reminder.
Panicking, Jack rouses his crew and has them sail to the nearest bit of land, without explaining himself. So great is his fear that when his beloved tricorn hat is sent overboard in the confusion, he doesn’t bother trying to retrieve it. The hat is later found by a pair of sailors onboard a sloop, who fool around with it before they feel the ship shake. Seconds later, the sloop is violently dragged underwater by an unseen force.
Elsewhere, Will sets off to find Jack, and eventually tracks the Black Pearl to Isla de Pelegosto, an island inhabited by a tribe of cannibals. Will is captured by the Pelegostos and bought before Jack, who has inexplicably been made chief of the tribe. Jack feigns ignorance of who Will is and orders him taken away, but also gives the man a whispered request to save him.
Back in Port Royal, Elizabeth is broken out of jail by her father, Governor Weatherby Swann, who is skeptical of Will’s chances of returning with Jack’s compass. Governor Swann attempts to get his daughter onto a ship sailing to England, but they are intercepted by Ian Mercer, Becket’s dragon. Elizabeth manages to escape and break into Beckett’s office, where she holds him at gunpoint and forces him to sign and seal the papers he had planned to offer Jack, intending to take them to Will. Before she leaves, Beckett warns her that he will still be after the compass.
On Isla de Pelegosto, Pintel and Ragetti, two of Barbossa’s mooks from the previous film, come across the Black Pearl following their escape from prison. Will meanwhile finds himself caged with the surviving members of the Black Pearl’s crew, including Jack’s first mate Joshamee Gibbs, who explains that Jack must behave in a certain way if he wants to keep control of the Pelegostos. He also warns that the Pelegostos believe Jack to be a god in human form, and are planning to cook and eat him later on. Jack and his crew make their own separate escape attempts and reunite at the beached Black Pearl, which Pintel and Ragetti had been in the process of stealing, and the survivors manage to escape from the cannibals. Will reveals Elizabeth’s predicament and demands Jack’s compass following the escape, but Jack offers to give him the compass in exchange for the key he’s currently looking for.
Jack, Will and the crew visit Tia Dalma, a mystic living on Isla de Pelegosto and the original owner of Jack’s compass, for more information about the key. After learning that the compass isn’t helping him find the key, Tia Dalma remarks that Jack either doesn’t know what he wants, or doesn’t want to claim it as his own. She reveals that the key unlocks the titular Dead Man’s Chest, which contains the heart of Jones; after falling in love with a woman “as cold, harsh and untamable as the sea”, he was betrayed by her and unable to bear said betrayal, thus he carved out his heart and locked it away. The heart is still keeping Jones alive, and Jack realizes that he can use the heart to force Jones to leave him alone. Before Will and the pirates leave, Tia Dalma discovers the black spot Jack bears, and gives him a jar of dirt as protection from Jones, who can only step on land once every decade.
Following directions from Tia Dalma, the Black Pearl sails to a rock formation where a ship has run aground. Jack tells Will that the ship is the Flying Dutchman, before instructing him to row there and find the key. He also adds that if caught, Will should claim he was sent to settle Jack’s debt. Will travels to the destroyed ship, where he learns that the crew were attacked by the kraken, shortly before the actual crew of the Dutchman - humanoids resembling anthropomorphic sea creatures - appear and capture all aboard. Jones himself - a humanoid fusion of a man, octopus and crab - arrives soon afterwards and offers the captured men a hundred years of service aboard the Dutchman as an alternative to certain death. Will tells Jones the story Jack gave him, and Jones, spotting the Pearl nearby, teleports aboard it and negotiates a new deal; if Jack can gather one hundred souls (including Will) within three days, Jones will forgive the original debt.
Pressed into service aboard the Dutchman, Will finds himself reunited with his father, who reveals that Jones’s offer has a downside; besides the aquatic transformations, those who take it slowly lose their minds, and eventually become part of the Dutchman. Will learns from one such member of the crew that Jones possesses the key he was looking for, but claims both it and the chest are hidden.
The crew of the Black Pearl head to Tortuga in the hope of recruiting the remaining ninety-nine souls. While there, Jack re-encounters James Norrington, who has lost his commodore position and standing in the Royal Navy after he both gave the pirate a day’s head start in escaping justice at the end of the previous film, and lost his ship in an offscreen hurricane while trying to catch the Pearl later. Elizabeth is also there, having disguised herself as a man to sail onboard a merchant vessel, and tricked the crew into sailing to Tortuga. Jack recruits both of them, admitting to Elizabeth that Will is Jones’s prisoner, but denying his role in it. He reveals to Elizabeth that his compass points its bearer to whatever they want most; by giving it to Elizabeth and convincing her that finding the Dead Man’s Chest will save Will’s life, she is able to use it to pinpoint the location of the chest.
Aboard the Dutchman, Will observes members of the crew playing Liar’s Dice while gambling their remaining years of service. Learning that any member of the crew can be challenged, Will challenges Jones for the key, offering an eternity of service beyond his original century if he loses. Jones agrees to wager Will’s remaining service in place of the key, but also reveals that he keeps it upon his person. Bootstrap joins the game while matching his son’s wager, and later makes a suicidal bid to keep Will from losing, condemning himself to an eternity aboard the Dutchman in exchange for Will’s freedom. Will however reveals that the true purpose of the game was to find where the key was located, making Bootstrap’s actions a Senseless Sacrifice. Nevertheless, Will later pickpockets the key from Jones and escapes the Dutchman, after vowing to kill Jones and free his father.
As the Black Pearl approaches Isla Cruces, the location of the Dead Man’s Chest, Jack, Gibbs and Elizabeth bring each other up to speed on the actions of Will and Beckett, with Norrington listening in. The pirates deduce that Beckett’s goal had always been the chest; with Jones’s heart, the East India Trading Company would have the Dutchman at their beck and call, allowing them control over the seas and the ability to crush pirates with ease. Norrington takes interest in the letters of marque Beckett had planned to offer Jack, and hints to Elizabeth that Jack might have been responsible for Will’s fate. Jack and Elizabeth later flirt with each other, before the black spot reappears on Jack’s hand, signifying Jones’s discovery of both the key’s theft, and Jack and Will’s deception.
The Dutchman tracks Will to the merchantman Elizabeth had traveled to Tortuga on, and Jones forces Bootstrap to watch as the Kraken is summoned to destroy it. Will and the ship’s crew put up a valiant fight, but the ship is inevitably destroyed, though Will manages to survive and hide onboard the Dutchman. Jones then has the ship sail to Isla Cruces, knowing that Jack is after the chest.
Reaching the island, Jack, Elizabeth, Norrington, Pintel and Ragetti locate and dig up the Dead Man’s Chest. Before any of them can open it, Will shows up and reveals both Jack’s role in getting him stuck on the Dutchman, and his intention to stab the heart and free his father. Jack draws a sword on Will, believing that with Jones dead, there will be no-one to call off the Kraken. Will grabs Elizabeth’s sword to challenge Jack, but Norrington draws his own sword on both of them, intending to deliver both the heart and the letters of marque to Beckett in order to regain his naval career. A three-way duel over the key ensues; while the three men are distracted, Pintel and Ragetti steal the chest for themselves, with Elizabeth giving chase afterwards.
Elizabeth, Pintel and Ragetti are later attacked and chased by Jones’s crew, dropping the chest in the chaos. Meanwhile, the fight between Jack, Will and Norrington moves to an abandoned water mill, and then onto the mill’s water wheel, which gets broken away and sent rolling across the island as the three men fight on top of - and within - it. Jack ultimately manages to get hold of both the key and the chest, retrieving the heart and returning to the dinghy he and his crewmates arrived in.
Jack hides the heart in his jar of dirt. Before he can escape, he gets attacked by one of Jones’s crew, and everyone else soon converges upon the pair, with Pintel and Ragetti having regained the now empty chest. Norrington makes it back to the dinghy first, and while Jack’s distracted, he discovers both the letters of marque, as well as a bit of dirt from Jack’s jar spilled within the boat. When he and the others find themselves surrounded and outnumbered by Jones’s crew, he takes the chest and flees back inland, acting as a lure for the monstrous pirates and allowing the rest to get back to the Pearl. He later tosses the chest to Jones’s crew and makes his own escape.
Back on the Pearl, Jack, Will, Elizabeth and Jack’s crew find themselves confronted by the Dutchman. After an entertaining bit of taunting with the dirt jar on the part of Jack, Jones attempts to sink the Pearl with the Dutchman’s cannons. Unfortunately for him, the Black Pearl happens to be the one ship capable of outrunning his own, and it does just that. Not that this is a serious setback for him, as he just calls forth the kraken again. Meanwhile, Will proposes they turn and fight the Dutchman with their faster ship, but Jack suggests they negotiate instead, indicating the jar of dirt.
And then the kraken grabs the ship, jolting it. This causes the jar of dirt to fall and break…and there’s nothing but dirt inside. Jack is shocked.
Now without any leverage, the crew of the Pearl attempt to repel the Kraken, but despite their best efforts - and Will devising tactics based on his previous encounter with the monster - they’re killed one after the other. Seeing the situation as hopeless, Jack attempts to flee in the Pearl’s remaining dinghy, but has a change of heart and returns just in time to shoot a net full of gunpowder and rum that had been set up to use against the Kraken, blowing it up and hurting the monster, forcing it to retreat. The survivors - Jack, Will, Elizabeth, Gibbs, Pintell and Ragetti, as well as side characters Cotton and Marty - realize that even this will not be enough to put the Kraken down, and Jack gives the order to abandon ship, in the faint hope that they can get to nearby land in the dinghy.
While the others get ready to leave, Elizabeth approaches Jack and thanks him for returning to save them…before kissing him. He kisses back. Will sees this, and is shocked.
Still continuing to kiss Jack, Elizabeth guides him towards one of the Pearl’s masts, out of sight of Will and the others…and then she chains him to it. She knows that Jack’s the target of both Jones and the Kraken; the only way she and the others can survive is to give him up. Jack commends her for her thinking, and Elizabeth joins the others in the dinghy. Unaware that Will saw her kissing another man, Elizabeth lies and claims that Jack chose to stay behind and make a Heroic Sacrifice.
As the dinghy rows away, Jack manages to get free, takes up his sword, and makes his Last Stand against the Kraken as it pulls the Pearl under the waves. Watching this occur, Jones declares his debt with Jack settled, and then has the retrieved chest bought before him. His happiness turns to rage when he discovers the chest empty; he tilts his head back and screams “DAMN YOU, JACK SPARROW!” to the heavens.
Of course, Jack’s not quite the one responsible here. Back in Beckett’s office, Norrington presents the signed and sealed letters of marque he retrieved from the dinghy to the head of the East India Trading Company. Beckett asks if he intends to trade Jack’s compass for the letters, but Norrington states that he has something better to offer, before dropping the heart of Davy Jones onto Beckett’s desk.
Back on Isla de Pelegosto, Tia Dalma’s hideaway plays host to a funeral held in Jack’s honor. Seeing Elizabeth’s downcast state, Will assumes she’s mourning a lover, and begins to tell her that if anything could be done to bring Jack back…before Tia Dalma cuts in and asks if he’d do such a thing. She puts the question to the rest of the crew, asking if they’d sail beyond the edge of the Earth to bring back Jack and the Pearl. All gathered agree, even Will, and Tia Dalma states that they’ll need a captain who knows such shores…
…at which point, none other than the formerly dead Hector Barbossa enters the room, much to the shock of everyone bar Tia Dalma. As they all gawp, Barbossa asks cheerily what’s become of his ship, before taking a bite from an apple and smirking.
