Marnie and Dylan are going to follow their dreams to go to college, at Halloweentown University, which is also known as Witch University.
Marnie and Dylan have graduated high school and are now going to go to college at Witch U in Halloweentown. Marnie is offered a full scholarship, Marni's mother, Gwen of course does not want her daughter at school in Halloweentown so she forces Dylan to tag along. At the school, witches and warlocks can't use magic. Marnie soon makes a new friend named Aneesa, whom is a genie. Marnie soon discovers that she is partly to blame for the rules against the use of magic at school. At one point a box, with the name "S. Cromwell" inscribed on it, magically appears in front of her. Most people at the school believe that Marnie used her magic to conjure up the box, but it was brought to her by fate.—Anonymous
Marnie is offered a scholarship to study at Witch University, her mother wants her to go to college in the Mortal World. Gwen forces Dylan to tag along. She meets a genie named Aneesa. She finds a box that says,"S.Cromwell."She learns her grandmother's true identity.She has to choose to either use the Cromwell Gift or not.
One year after the events of the last film, an eighteen-year-old Marnie receives a full scholarship to Halloweentown's Witch University, headed by Chancellor Luxana Goodwyn, due to her good deeds in previous years. Much to her mother Gwen's dismay, Marnie decides to abandon her original college plans and attend the Halloweentown school instead. Gwen forces Marnie's brother, Dylan, to accompany her and keep an eye on her.
However, the school is not what it seems. Witches and warlocks are prohibited from using magic; instead, the curriculum resembles that of a mortal college, focusing on subjects like Shakespeare analysis and the history of old magic. Marnie, who expected to learn how to use her magical abilities, is left disappointed.
At Witch University, Marnie reunites with her old friend Ethan and makes a new friend named Aneesa the Genie. She also encounters three new adversaries: the Sinister Sisters-Scarlett, Sapphire, and Sage. These manipulative and snobbish witches are the daughters of Silas Sinister, and they quickly capture Dylan's admiration. Marnie learns that she is responsible for the university's restriction on magic. Originally, the university was established for witches and warlocks to learn magic, but when the portal between Halloweentown and the human world opened permanently, most magical beings opted to study in the mortal realm. Consequently, Witch University allowed other magical creatures to enroll and banned magic on campus to maintain a level academic playing field. The Sinister Sisters, however, continue to use their powers discreetly.
Classes prove dull for Marnie until a session with Dr. Ichabod Grogg leads her to discover a box inscribed with the name "S. Cromwell," which magically appears before her but is locked without a key. Seeking answers, Marnie approaches one of her professors, Miss Periwinkle, who reveals that "S" stands for Splendora and that they were very good friends. Marnie and Dylan learn that the box contains the Gift-a magical power that only a Cromwell can wield-which Splendora locked away centuries ago.
Meanwhile, the Sinister Sisters exploit Dylan's infatuation with them to make him do their homework and use him to bait Marnie. Later, Ethan shares information about a mysterious group called the Dominion, of which his father was part. He warns Marnie that they intend to use her to unlock the box and seize the Gift to take over Halloweentown, turning everyone into their slaves. Although Marnie initially doubts Ethan's claims, she eventually travels to the past to meet Splendora and learn the true nature of the Gift. Splendora explains that the Gift is an amulet that grants the wearer the power to control others-a forbidden power for witches, capable of tempting a good witch to turn bad. Marnie realizes Ethan was right about the Dominion, and Splendora gives her the key to the box containing the Gift. It is revealed that Splendora is actually Marnie's grandmother, Aggie, who dropped the name "Splendora" long ago.
Returning to the present with the key, Marnie discovers that Dr. Goodwyn has stolen the Gift for the Dominion and the Sinister Sisters in order to take over Halloweentown. Knowing only a Cromwell can wield the Gift, the Sinister Sisters transform Dylan into a Border Collie to coerce Marnie into compliance. They agree to revert Dylan to his natural form if Marnie agrees to help them control Halloweentown. Marnie pretends to cooperate, initially using the Gift to manipulate the people at Witch University, but ultimately turns against them. With Aneesa's help, she traps the Gift in her lamp.
Marnie, Dylan, Gwen, and Aneesa then destroy the lamp, which eliminates the Gift. The Dominion attempts to escape but is apprehended by Periwinkle, who is revealed to have been an undercover agent for the Halloweentown Anti-Dominion League for ten centuries. She imprisons the Dominion in a Witch's Glass, stripping them of their magic and charging them with treason.
The Sinister Sisters also lose their powers, but Marnie learns that Ethan willingly gave up his powers after his father was found guilty in the previous film. Marnie and Ethan begin a new relationship and leave on a date. Marnie secretly reveals to Gwen that she did not actually destroy the Gift; instead, she entrusted it to someone she completely trusts. The film concludes with Dylan discovering that Marnie left the Gift for him in a book he was reading. As spells cast on the grounds of Witch University become permanent at midnight, the Gift now belongs to him, as he is the only person Marnie trusts with its power. Reserved for important purposes only, he puts the book away, revealing a glowing red "S" at the end of the film.
