A pair of fishermen on their boat of the coast of Spain pull an old man out of the ocean who became entangled in their fishing net. He gasps “Ponce de Leon” and the men quickly sail to shore and bring him to the Spanish monarch. The young monarch learns of the Fountain of Youth and demands that his men set sail at once to find the ship.
In England, a pair of guards escort a masked prisoner into a loud courtroom which is holding the trail of Captain Jack Sparrow. The prisoner is brought in and mask is removed to reveal that the prisoner is none other than Joshamee Gibbs (Kevin McNally), Sparrow’s first mate. He tries to convince the people he’s not Jack Sparrow, but the crowd demands blood and calls for a hanging. The court allows the judge to enter the proceedings and Gibbs is surprised to see that it’s Jack dressed like the judge. Jack commutes Gibb’s sentence to life in prison, bribes the carriage driver and gets into the prisoner carriage with Gibbs.
Jack explains that he returned to London as soon as he heard about Gibbs’ capture. Gibbs tells Jack that someone claiming to be Jack Sparrow is looking for people to join his crew and that he was mistakenly captured when he arrived at the bar. Jack is confused and tells Gibbs that he isn’t looking for a crew. He shows Gibbs the map to the Fountain and tells him that he hit a bit of a snag trying to locate it. As the two finish talking the carriage stops and the door opens to reveal several soldiers pointing their guns at the pair.
Jack is escorted to the chambers of King George. The King does not want the Spanish monarchs, a “bunch of Catholics” to have control over the Fountain of Youth and wants Jack to guide a ship to the Fountain. The king’s privateer peg legged privateer captain enters the room and is none other than Hector Barbossa. Jack is furious to learn that Barbossa “lost” the Black Pearl at sea with his leg and angrily insists that Barbossa should join it. The King asks Jack if he has the map and Jack realizes that Gibbs took it while they were in the carriage. He organizes a complex escape from the room and the building. The guards pursue him through London by carriage until Jack final gives most of them the slip by jumping off of his carriage. He turns around to find a guard pointing a gun at him but the guard is quickly shot by Captain Teague (Keith Richards), Jack’s father.
Teague takes Jack to the bar where the imposter Jack is organizing a crew. Teague asks Jack if he knows anything about the ritual of the Fountain and warns Jack of the tests that will lie in his path. He points out the men who have joined the crew and have a ship and disappears, leaving Jack to his own devices.
Jack confronts the men who in turn believe Jack to be an imposter. He sees the imposter by an adjacent door and follows him. The two duel for a bit before Jack recognizes the fighting style of the imposter, and going straight for a kiss. He pulls the fake beard off of his opponents face and asks Angelika (Penelope Cruz) what she thinks she’s doing. Angelika explains that she’s after the Fountain and needs a crew to get it. She asks Jack if he still has the map and he tells her that he memorized it. Jack apologizes for ruining her life by preventing her from taking her vows and says that he honestly mistook her convent for a brothel, a mistake anyone could have made. Before they can go at it again, British soldiers arrive hunting for Jack. Jack and Angelika fight them all and eventually dive down a cellar which leads out into the Thames. They climb out and get back to shore but Jack is knocked out by a tainted dart while asking Angelika about the ritual of Fountain.
When Jack comes to he finds himself aboard the Queen Anne’s Revenge, the ship of the feared pirate Edward Teach popularly referred to by his nickname, Blackbeard. Jack is furious to have been conscripted into helping Blackbeard, a ruthless killer. Angelika explains that Blackbeard believes her to be his daughter and that she is desperate to find the Fountain and that Jack will be their compass. Jack sees a man strapped to the top of the mast and is told by a fellow crewman that the man is part of the clergy, allowed to live only by Blackbeard’s grace.
That night, Jack organizes a mutiny against Blackbeard by convincing the crew that, since they haven’t seen Blackbeard, Blackbeard is not really on the ship or even captaining it. The men rise up and Jack frees the missionary, a young man named Phillip, from the mast. The commotion awakens Blackbeard (Ian McShane) who uses his sword to bring his ship to life, using the ropes on the sails to capture the mutineers. He makes an example out of a young man by throwing him off the ship in a lifeboat and using the ship’s flamethrower to ignite the little boat, a warning to the crew that anyone who stands against him will be killed.
Back in England, Gibbs is brought before Barbossa to be hung. Barbossa tells Gibbs to give him the map he stole from Jack. Gibbs takes out the map and throws it into a nearby fire pit, telling Barbossa that the only way Barbossa will find the Fountain of Youth is if Barbossa agrees to keep Gibbs alive and use him as the ship’s navigator. Barbossa begrudgingly agrees and welcomes Gibbs back into the Royal Navy.
On Blackbeard’s ship, Jack tries to convince him that Angelika is lying about being Blackbeard’s daughter but Blackbeard confirms that she is actually his child. Blackbeard tells Jack about a prophecy which foretold Blackbeard’s death at the hands of a one legged man. Jack is tortured for a bit using a voodoo doll but Blackbeard relents when Angelika intercedes on Jack’s behalf. She tells him in private that the ritual to use the Fountain involves a mermaid’s tear and two silver chalices from the ship of Ponce de Leon, which contain the key to finding the Fountain. She explains that the Fountain takes life from one drinker and gives it to the one who drinks from the cup with the mermaid tear. Angelika takes him into Blackbeard’s treasure room and shows Jack that Blackbeard captures enemy ships and places them in magic bottles. She shows him what became of his beloved ship, the Black Pearl.
The Queen Anne’s Revenge pulls into White Foam Cove and the crew is put into lifeboats to begin hunting for mermaids. Blackbeard lands on shore with Jack and Angelika and they ignite a lighthouse in order to attract the mermaids with the light. Phillip is out at sea on the lifeboat when the mermaids start to arrive and enchant the sailors. A mermaid drags one of the sailors under and soon all of the mermaids are attacking the boats. Blackbeard uses the Queen Anne’s Revenge to begin driving the mermaids to shore and Phillip uses the distraction to dive into the water and desperately begin swimming to shore.
Meanwhile, the mermaids have begun using their hair to drag people on shore in to the water to kill them. Angelika is grabbed by the leg but Jack jumps over her and cuts the hair with his sword. Realizing that Blackbeard’s plan will get them all killed, he races to the lighthouse and damages the support beams enough to cause it to implode. He dives into the water just as debris falls all around him. Phillip reaches the shore around this time and is about to be crushed by falling debris when he is knocked aside by a mermaid. The mermaid’s tail gets crushed, pinning her to the ground. Phillip releases it, but when she tries to escape he stabs her in the fin in time for Blackbeard to come and capture her.
The mermaid is placed in a glass coffin and the men journey into the heart of the island looking for the lost ship of Ponce de Leon. Phillip sees that the mermaid is suffocating because she can’t get any air in the sealed coffin. He resists Blackbeard’s orders and pries the coffin open with his sword, wedging his bible in enough to keep the coffin from closing. His concern for her touches the young mermaid, who is unsure what to make of Phillip.
The group reaches a giant gap in the land which means that someone has to go on ahead without the others and find the ship. Blackbeard tells Jack that if Jack doesn’t go, Blackbeard will kill Angelika. Jack laughs at the idea but Blackbeard tells his men to bring 6 pistols, two of which have bullets. Jack takes one and fires it at Angelika but its empty. Blackbeard makes Jack choose again and Jack takes one, sure that it isn’t loaded and fires it into the sky, blowing off a branch off a tree. Jack is mortified and Angelika is slightly disturbed but Jack agrees to go on alone. He asks Blackbeard’s Voodoo servant if he will survive the jump. The Voodoo Priest tosses and effigy of Jack off the cliff and says “Now you will survive.” Jack dives in and goes it alone.
Barbossa and his men arrive at the shore in lifeboats and see the remnants of the mermaids who were killed on shore. Their main ship is soon overrun by mermaids and Barbossa tells the remaining men that they are going on, ignoring the screams of the men being ripped apart on the ship.
Phillip and Blackbeard’s men get into an argument and Blackbeard’s men drop the mermaid’s coffin. They are surprised to see that upon touching land, the mermaid’s tail dissolves and she is left with normal legs. Phillip takes off his shirt and covers her with it, then carries her. He names her Syrena so that the group will have a name for her. Blackbeard takes Syrena to a special pool, where mermaids are tortured and left for dead. He demands that she cry but she does not shed a tear. Realizing that Syrena probably has feelings for Phillip, Blackbeard has his men stab him in front of her and toss his body in the woods. Phillip comes to hours later and removes a knock out dart from his neck, groggily stumbling back to the pit. He tries to free Syrena, who begins crying tears of joy, but Blackbeard appears and knocks Phillip out, bottling the tear. He has his men drag Phillip away and leaves Syrena to die.
Jack arrives at the ship of Ponce de Leon, which is delicately balanced on the point of a mountain. The slightest shift in weight will send the ship hurtling to the bottom of a crevice and kill whoever is inside. Jack tries to find the silver cups but is surprised by Barbossa, who was lying in wait. Barbossa explains that the Black Pearl came alive because of Blackbeard’s sword and that he was forced to cut his own leg off to escape the ship. Jack is surprised but agrees to help Barbossa kill Blackbeard. They find the chalice box but see that it is empty The Spaniards have beaten them to it. Using the map of Ponce de Leon, they deduce the only area for the Spaniards to make camp and head out.
The duo steals the cups and Jack realizes that Barbossa’s sword has a distinct smell to it. Barbossa calmly explains that he has been killing poisonous frogs with his sword and plans to use the toxin to kill Blackbeard. They fail to retrieve the cup and are instead captured and tied to posts. Jack escapes and leads the Spaniards on a chase while Gibbs and Barbossa’s men rescue Barbossa and steal the cups. Jack tells Barbossa how to follow them to the Fountain and they part ways, Gibbs joining Jack for the final leg of the journey.
Jack and Gibbs find Blackbeard’s group and they look for the location of the Fountain: The cave where water falls up. Jack finds it and leads the men through, knocking the cups together. Blackbeard grows impatient and threatens to shoot Jack but Jack realizes that the inscription on the cup is the password to the pool. He says the magic words and a pool forms on the ceiling of the cavern. Jack jumps up and climbs through and looks around the Fountain room. Blackbeard and his men follow but are soon ambushed by Barbossa’s men and a full scale battle erupts. Phillip uses the distraction to cut his bonds and escape, but gets stabbed in the stomach on his way out of the Fountain.
Jack and Angelika fight over the chalices and tear because Jack doesn’t want her to give it to Blackbeard. Meanwhile, Blackbeard gets the upper hand on Barbossa and is about to kill him when the Spaniards arrive and begin destroying the Fountain, not wanting a pagan monument standing the way of God. They throw the chalices into the pool and Barbossa takes the opportunity to stab Blackbeard in the back with the poisoned sword. Angelika freaks out and pulls the blade out, cutting her hand in the process. Barbossa takes Blackbeard’s sword as payment for his leg and tells Blackbeard’s men that they are now his.
Phillip arrives at the pit where Syrena has been chained and he begs God to save her life, even at the cost of his own. He cuts her bonds and she immediately swims away, heading straight for the pool room.
Jack realizes that Angelika only has moments to live. He desperately seeks the chalices in the water but they are out of reach. Syrena arrives carrying the chalices and tells him not to waste her tear before she leaves. Jack grabs the chalices and puts water from the Fountain into them and places the tear in one of the cups. He goes to Blackbeard and tells him that he needs to save Angelika’s life as a good father would. Blackbeard takes the wrong cup, determined to survive and drinks. Angelika is both disappointed and happy but Jack interrupts Blackbeard’s celebration by pointing out that he gave Blackbeard the wrong cup. The pool surrounds Blackbeard and rips him apart, transferring his life to Angelika’s.
Phillip lies dying by the pool and Syrena returns to him. She tells him that she can save him but Phillip only wants her forgiveness. They kiss and Syrena drags Phillip to the bottom of the sea.
Angelika is pissed with Jack for killing her father but Jack is unrepentant. He ties her up and brings her to the same island he was marooned on years before and he tosses her a pistol with a single shot. She fires it at him and misses as Jack prepares to leave her. He suggests that he loves her before rowing away.
Barbossa takes the Queen Anne’s Revenge and sails off with his new crew. Gibbs, on the shore of the island, awaits Jack’s return. The two meet and Gibbs hands Jack a big: Gibbs went to the Queen Anne’s Revenge stole Blackbeard’s collection of ships trapped in bottles: Jack is now free to have the Black Pearl and a fleet of pirate ships at his disposal.
Angleika is seen sitting on the island near shore. Suddenly she looks up seeing something in the water. As she walks down to the water we see Jack's voo-doo doll wash up on shore, Angelika picks up the doll and smiles
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