To control the oceans, Lord Cutler Beckett executes anyone associated with piracy by ordering Davy Jones to destroy all pirate ships in the seas. Condemned prisoners sing "Hoist the Colours" to compel the nine Pirate Lords to convene at Shipwreck Cove to hold the Brethren Court. Because Captain Jack Sparrow, one of the Pirate Lords, never named a successor before being killed, Captain Barbossa, along with Will Turner, Elizabeth Swann, Tia Dalma, and the crew of the Black Pearl, plot to rescue Jack from Davy Jones's Locker. Traveling to Singapore, the crew meet Captain Sao Feng, who owns navigational charts to the Locker and quickly gains an unpredictable interest in Elizabeth. Beckett's soldiers invade, but the crew escape. Feng and Turner make a deal to give Jack to Feng, so he in turn can use the Pearl to rescue his father Bootstrap Bill from the Flying Dutchman. The crew travels to the locker and rescues the marooned Jack. They find themselves trapped, encountering dead souls, including Elizabeth's father Governor Swann. They learn the Dutchman must always have a captain.
Returning to the living world, the Pearl is attacked by Sao Feng and Beckett's men. Through a complex series of deals, Elizabeth is handed over to Feng, who believes she is the goddess Calypso, while the rest of the crew make for Shipwreck Cove aboard the Pearl, though Jack later throws Will off the ship as part of the 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. He plans to release her to defeat Beckett. Davy Jones attacks Feng's ship, but Feng appoints Elizabeth his successor as Pirate Lord before dying. Admiral Norrington frees Elizabeth and her new crew from the Dutchman, but is killed by a crazed Bootstrap Bill.
The Black Pearl arrives at Shipwreck Cove where Barbossa attempts to persuade the Brethren Court to release Calypso. Davy Jones visits Tia Dalma in the Pearl's crew. Jones attacks the Pearl with the Kraken, which devours most of the crew and destroys all but one of the Pearl's brig, revealing she is Calypso, and they promise to be together again. Jack's father Captain Teague and Keeper of the Pirate Code, informs the Court that only an elected Pirate King can decide. A vote is taken. To avoid a stalemate, Jack casts his vote for Elizabeth, making her King.
The Brethren Court and Beckett's fleets emerge for war. On a sandbank, Elizabeth, Jack, Barbossa, Beckett, Jones, and Will parley, trading Will for Jack, and Barbossa steals Jack's piece of eight, all of which are owned by the Pirate Lords and required to free Calypso. Barbossa frees Calypso, but when Will reveals it was Jones who made it possible for the first Court to imprison her, Calypso vanishes and summons an enormous maelstrom.
The Pearl and the Dutchman battle in the maelstrom. And Ernie uses the Red Orb to summon Kyogre, in order to defeat our heroes. And then the Orb is being absorbed into Archie and takes control of him, as he has blue marks. But then Eevee gets more crazier, and out of the water comes, Groudon! Eevee jumps onto Groudon's head, and Ernie orders Kyogre to wipe them out with a tidal wave, but Groudon stops it with a Solar Beam. Brian now realizes that Groudon wants to stop Kyogre. He states the orb absorbed into Eevee was made to let Groudon ask Eevee to help it fight Kyogre. Groudon waves its claw and launches a shock wave, which hits Kyogre. Brian states he'll stop Kyogre, no matter what it takes. Elizabeth and Will are wed by Barbossa before swinging over to the Dutchman to aid Jack. On board the Dutchman, Jones and Jack engage in a duel, with Jones gaining the upper hand. Kyogre fires a Hydro Pump, but Eevee stops it with a Thunder shock attack. Sylveon tells him not to do anything crazy, Brian promises her he won't and he goes to try to help Eevee. Jones stabs Will with a sword, causing Bootstrap to fly into a rage and attack Jones. Jones begins to gain the upper hand, but Jack and Elizabeth help Will stab Jones' heart. Jones dies and falls into the maelstrom, while Will succumbs to his injuries. Groudon uses Solar Beam, hurting Kyogre and stopping the waves Kyogre tried to summon. With Kyogre severely wounded, the Red Orb leaves Ernie's body. Ernie falls, and passes out. Groudon roars and the Blue Orb leaves Eevee's body as well. Eevee unconsciously falls down into the ocean, bur Brian dives after him. Jack and Elizabeth, and our heroes escape the Dutchman as it is sucked into the maelstrom, while the crew of the Dutchman converge on Will, led by Bootstrap.
As Beckett's ship, the Endeavour, approaches to destroy the Pearl, the Dutchman rises, now captained by Will, and the crew free of Jones' curse. And Brian and Eevee come out of the water with Kyogre's help, along with Groudon. Together, the two pirate ships destroy the Endeavour, with a stunned Beckett going down with the ship while his navy retreats, demoralized by the loss of both the Endeavor and their commander in Beckett. And Kyogre uses Hyper Beam to kill Ernie, while the Dazzlings retreat. Suddenly, the two Orbs go up in the air, merging and vanishing into dust. And Groudon and Kyogre both go back to their natural homes, respectably. As Sylveon hugs Eevee with delight that he's okay. With Will now bound to escort souls lost at sea to the next world for ten years, he and Elizabeth consummate their marriage before he departs on the Dutchman.
Jack and Joshamee Gibbs discover Barbossa has stolen the Black Pearl again, but Jack planned ahead and cut out Sao Feng's navigational charts, departing from Tortuga alone to track down the mythical Fountain of Youth to become immortal.
In a post-credits scene, set ten years later, Elizabeth and her son watch from a sea cliff as Will returns aboard the Dutchman.
- Peter Griffin, Belle, Shining Armor, Princess Cadance, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, Mitzi, Buttercream Sunday, Roger Smith, Bender Bending Rodríguez, Minerva Mink, Judy Hopps, and Nick Wilde guest star in this film.
- The Dazzlings and Ernie the Giant Chicken will work for Davy Jones in this film.
- Beauty and the Beast, Zootopia, and Pirates of the Caribbean: At World's End are Disney films.
- The storyline continues in Brian and the Eeveelution Family's Adventures of Pirates of the Caribbean: On Stranger Tides.
- Kevin MacLeod - Relent (when Minerva Mink apologizes to Roger for her behavior)
- Kevin MacLeod - Hitman (during Groudon and Kyogre's battle)
- Pokémon Heroes - Sortie! (when Gordon blasts Kyogre)