At a sunny resort town, the Ghostly Trio’s mischief at a baseball game sends the crowd into a panic, and their nephew Casper, Jeremy Foley unable to settle the terrified spectators, watches as the park floods with emptiness. Satisfied by the chaos, Casper’s uncles decide to take a quiet vacation, hoping the break will calm everyone down and give them a chance to recharge their spooky reputation.
Meanwhile, a malevolent warlock named Desmond Spellman, George Hamilton is warned by the Oracle in the Mirror that in the future a good little witch named Wendy will surpass him. Desmond schemes to remove her from the equation through a cataclysmic weapon called the Mystic Abyss, a dimensional rift that can destroy living beings. He seeds his plan by creating two spies, Jules, Richard Moll, and Vincent, Vincent Schiavelli, and assigns them to bring Wendy to him from her country life, where she resides with three aunts: Gert, Gabby Shelley Duvall, and Fanny Teri Garr.
Jules and Vincent reach Wendy’s home and attempt to escort the young witch to Desmond, but Wendy narrowly escapes with her aunts. To keep Wendy safe, the group hides and ends up vacationing at the same resort where Casper and his uncles are staying. Wendy soon meets a boy named Josh Jackman, Blake Foster, who initially comes off as friendly but reveals a self-centered side by disregarding others at the arcade and ignoring Wendy when she tries to chat.
Casper and Wendy eventually cross paths again in a barn and strike up a tentative friendship, aware that their guardians are natural antagonists. The two hatch a plan to bring their caretakers together at a party. Casper convinces the Ghostly Trio to possess three men who resemble them, while Wendy persuades her aunts to attend the party disguised as regular guests so they can meet the men. The plan works briefly as the possessed men flirt with the witches, who are posing as ordinary women, and the two groups feel a spark of connection.
The ruse falls apart when the possession wears off and the ghostly impostors reveal themselves. Wendy’s aunts expose the ruse and threaten the Trio with magic, while Wendy explains that neither she nor her aunts can use high-level magic or Desmond will detect their location. Suspecting Casper is protecting the witches, the Trio pressure him to reveal their secret, and his hesitation leads them to terrorize Wendy and her guardians. Facing the threat, Wendy feels cornered and resorts to a high-level spell to plaster the Trio in place, which also signals Desmond to their location.
Casper’s betrayal of his promise to help leaves Wendy devastated and the two momentarily end their budding friendship. Casper returns to his uncles to plead for help, but the Trio stubbornly refuse, insisting Desmond is coming for the witches and that they should stay out of danger.
Desmond and his spies arrive at the resort, confront Wendy and her aunts, and outline the Oracle’s ominous prediction. When Wendy resists, Desmond summons the Mystic Abyss and casts Wendy into it, with Casper leaping in after her to try and rescue her. Inside the Abyss, Wendy apologizes for shouting at him and for ending their friendship. While Desmond’s forces clash with Wendy’s guardians, the Ghostly Trio—who initially seemed loyal to their own kind—find a new sense of purpose and inadvertently become crucial to the rescue when a giant three-eyed monster emerges and frightens Desmond so much that he trips and tumbles into the Abyss himself.
The monster proves to be the Ghostly Trio, who have had a change of heart, and they help hold the door to the Abyss open long enough for Wendy and Casper to escape. Exhausted and unconscious from their time inside the Abyss, Casper and Wendy are revived and cared for by their guardians. A heartfelt reunion follows, with the Ghostly Trio and Wendy’s aunts setting aside old rivalries to celebrate their teamwork and courage. The Oracle proclaims Wendy the greatest witch for achieving something no witch before her had—befriending a ghost.
Eventually, everyone prepares to bid farewell. Wendy and her aunts fly home to their own realm, and Casper and his uncles return to their spooky business, knowing their paths may cross again. Wendy grants Casper a shy goodbye kiss before departure, leaving him flushed with a mix of surprise and warmth, and the two friends part with the promise that they will see each other again very soon.