Sora, Donald, and Goofy find themselves out on the sea again, but they suddenly encounter a waterfall. After falling off it, they go unconscious, and when they wake up, they find themselves in an endless desert. They walk for a while until they find a ship floating above the sand. While running after it, they encounter Jack Sparrow. They help him catch the ship, which turns out to be the Black Pearl, and they manage to get it into some water. On the shore, they encounter a group of people. To the shock of Sora and friends, Hector Barbossa, whom they defeated the first time they visited the world, is among them, but Jack treats him like an old friend despite everything that happened last time. Will and Elizabeth are also in the group. They explain that Jack had a debt to Davy Jones that he failed to repay, so Jones sent the monstrous Kraken to devour him, sending him to Davy Jones's Locker.
Will tells Jack that a man named Cutler Beckett, the head of the British East India Company, took Davy Jones's heart, which he is trying to use to conquer the sea. The group takes the Black Pearl out to sea, where a woman named Tia Dalma explains what happened to Jack: he made a deal with Davy Jones. The deal stipulated that Jones would bring the Black Pearl, which had sunk sometime after they left the world, but Jack could only have it back for thirteen years. In exchange, Jack had to give up his soul, but he failed to uphold his end of the bargain, which caused Jones to send out the Kraken to collect his payment. Tia Dalma also says that, in order to escape from ones, Jack has to find a box, which catches the attention of Sora and friends, as they are reminded of the black box Maleficent is searching for. Tia Dalma tells them that the box contains the heart of Davy Jones himself.
Meanwhile, on another ship, Vexen and Luxord are scheming to take the box. Vexen is very interested in Davy Jones, who manages to continue living even without a heart, but Luxord has no interest in anything but carrying out his orders. Vexen says that the Organization must have accepted him back so he can continue his research, so he intends to do whatever is necessary in the pursuit of science. When Luxord tells him that he is simply being used by Xemnas, Vexen says that it doesn't really matter as long as he completes his goal of creating a perfect replica. Luxord reminds him that he knows this world better due to having been there before, so he asks Vexen to stay out of the way until he has dealt with Sora and his friends. Vexen agrees and vanishes.
The crew of the Black Pearl manages to return from Davy Jones's locker, but they are immediately attacked by another ship, which unleashes a horde of flying Heartless on them. Jack accuses Barbossa of summoning them, since he was the one who collaborated with Pete before, but Barbossa denies it. Tia Dalma whispers something to Sora, who uses the trails of smoke left by the Heartless to climb up into the sky. Sora defeats the big Heartless, known as the Raging Vulture, causing the smaller ones to explode as well. After the battle, Sora, who no longer has a way of staying airborne, plummets to the ground.
Sora is woken up by Donald and Goofy on an island, and Jack arrives shortly afterwards. In another scene, Jack is captured by Beckett, who offered to have Davy Jones forgive him if he told him everything he knew about the pirate organization known as the Brethren Court. They go to find a new ship, but while they are on their way, Sora thinks back to what Tia Dalma told him: she offered him all the power he could ever want if he freed her. Unfortunately, Sora isn't sure what she meant by "freeing" her. The group makes its way through an underwater cave, where they encounter a large Heartless called the Lightning Angler. After beating it, they find a ship called the Leviathan at the end of the cave. Part of the cave's wall crumbles, allowing them to steer it out of the island.
Shortly after making it outside, the Leviathan is stopped by Luxord's ship. Like before, Luxord calls parley before they can do anything, forcing them to negotiate. He tells them that he is looking for the box, and he offers them a contest: a race to Port Royal. If he wins, then Jack has to tell him everything he knows about the box, but if Jack wins, Luxord will give him anything he wants. Jack tells Sora and friends that the box is probably the one containing Davy Jones's heart. Assuming it to be the same black box that Maleficent mentioned, they resolve to win the race to prevent Organization XIII from getting closer to finding it.
Luxord sends out several smaller ships to impede the Leviathan's progress, but it still manages to win the race. Aboard Luxord's ship, when he asks Jack what he wants, he accidentally lets slip that the chest he's looking for is on board Davy Jones's ship, the Flying Dutchman. Luxord vanishes to go find it, sending Heartless to push them back onto the Leviathan. Sora wants to go after him, but Jack says they need to stop at Port Royal to repair the Leviathan first. When they reach the port, Jack tells them to look for white crabs, much to their confusion. After they find the crabs, Jack somehow uses them to repair the Leviathan. He reveals that he is actually a fake made by the goddess of the sea to help them; the real Jack is headed for a place called Shipwreck Cove, where he plans to confront Davy Jones and Cutler Beckett. The earlier scene where Beckett made a deal with Jack was what the real Jack was doing, while the fake one was with Sora and friends. The fake Jack proclaims Sora the captain of the Leviathan before bursting apart into hundreds of white crabs.
Meanwhile, at a place called Sandbar Isle, the real Jack, along with Elizabeth and Barbossa, confronts Beckett and Jones, who have taken Will hostage. Beckett is pleased with the deal he made with Jack, but Jones isn't satisfied; he wants Jack under his control. Elizabeth offers to give up Jack in exchange for Will, which Beckett accepts. He tells Elizabeth that they will spare a few of the pirates if they surrender, but she refuses. Shortly afterwards, the Leviathan approaches Shipwreck Cove, only to be stopped again by Luxord. He warns Sora that if he continues to act compulsively, he will eventually come to regret it. Luxord summons some more ships to attack the Interceptor, but they manage to destroy them.
At Shipwreck Cove, the Leviathan meets up with the Black Pearl. Will tells Sora that Jack has been taken by Beckett, and he also reveals that Tia Dalma was really Calypso, the goddess of the sea. Barbossa freed her so she would help them, but she seemingly did nothing. Sora, of course, realizes that the fake Jack was the help she gave them. Elizabeth gives a speech to rally the pirates for the upcoming battle while the Flying Dutchman appears on the other side. An enormous whirlpool forms in the sea which begins to suck the Black Pearl in. Luxord appears and sees the Flying Dutchman. Sora tells him that the box on the Dutchman has Davy Jones's heart, meaning that it can't be the black box he's looking for, but Luxord says that no one knows what's in the black box, meaning it could be the right one for all he knows. He tells Sora that he knows very little about the black box, only that it contains "hope." He summons the Kraken and has it rab the Black Pearl, so Sora is forced to man the Leviathan to beat it back.
The Leviathan manages to free the Black Pearl from the Kraken's grasp; meanwhile, Jack, who is aboard the Flying Dutchman, is trying to sneak away with the box. Luxord tries to take it from him, but Jack refuses. He attempts to invoke parley again, but Jack interrupts him, using his bad breath to cause Luxord to pass out and fall off the Dutchman. Jack tries to escape again, but Davy Jones stops him. Sora and friends show up to assist him, and together they fight Jones. Elizabeth and Will also join in, and Will manages to stab him through the chest, but without his heart he cannot be killed. While Jones goes after Will, Jack opens the box and prepares to stab his heart. From above, Vexen looks into the chest, realizing that it wasn't what he was looking for: the heart in the chest is Jones's physical, beating heart, not the spiritual heart that serves as the essence of one's self in the Kingdom Hearts series. Disappointed that it was the wrong box, Vexen vanishes. Jones stabs Will, and then Jack stabs his heart, causing him to die and fall into the whirlpool. Jack explains that the Flying Dutchman needs a captain; with Davy Jones gone, someone has to take its place, and that person is Will. Everyone else manages to escape, but Elizabeth has to be dragged back onto the Black Pearl.
Without Davy Jones, the whirlpool closes, but the pirates still have to deal with Beckett. He prepares to destroy the Black Pearl, but the day is saved when Will emerges aboard the Flying Dutchman. The Pearl and the Dutchman flank Beckett's ship, the Endeavour, and destroy it, putting an end to Beckett. Gibbs, one of Jack's crew members, tells Sora that as the captain of the Dutchman, Will is only allowed ashore once every ten years. Elizabeth goes to talk to Will for as long as she can before he has to leave. Jack says that even a short moment is enough to connect with someone, which Sora knows better than anyone. He vows to find the other Guardians of Light, and the Leviathan explodes into thousands of white crabs.
In the forest, Kairi approaches Lea with her new outfit. The two of them are excited because their training is almost over. Kairi says that if they can bring Roxas back, then they should be able to recover Naminé as well. Lea tells Kairi about how he met Ventus once when he was young. Because they only ever met once, he nearly forgot about the encounter, but then he met Roxas, who looks exactly like Ven. While Kairi and Lea are relaxing, Riku and Mickey have returned to the Realm of Darkness, where they are attacked by another Demon Tower.
Meanwhile, the two Ansems arrive at the Twilight Town mansion, where Hayner, Pence, and Olette are spying on them. Ansem the Wise wants to stop, but Ansem, Seeker of Darkness guilt trips him, blaming him for all the people who were lost during their research. Ansem the Wise explains that the reason he stopped his experiments in the first place is because the mysterious girl disappeared. Ansem SoD reminds him about what he did to Roxas and Naminé, and Ansem the Wise says that the only thing he wants is to atone for how he treated them. Hearing this, Hayner and his friends decide to rescue him. Ansem SoD says that the girl's memory will help him solve a mystery relating to the Keyblade War, but Ansem the Wise denies this.
Pence calls out to the Ansem SoD to create a distraction while Olette grabs Ansem the Wise to get him away. Hayner tries to attack Ansem SoD, but his Guardian stops him. The Guardian throws Hayner, but a Dusk appears and rescues him. Several other Dusks surround Ansem SoD and attack, allowing the others to escape. Ansem SoD realizes that if the Dusks are attacking him, someone in the Organization betrayed them. Meanwhile, Hayner and friends manage to get Ansem the Wise to safety. They ask him what he knows about Roxas, but before he can answer, they are approached by Vexen. He reveals that he was the one who sent the Dusks to rescue them, and much to his master's surprise, he also says that he wishes to atone for his crimes. With that, they begin to make their way back to Radiant Garden so Vexen can explain everything...
