In 1955, ten-year-old Lewis Barnavelt (Owen Vaccaro) arrives in New Zebedee, Michigan, to live with his uncle Jonathan (Jack Black) after a tragic car accident takes the lives of his parents. Upon his arrival at Jonathan’s home, Lewis quickly meets Florence Zimmerman (Cate Blanchett), Jonathan’s neighbor and dear friend, sparking an immediate rapport fueled by affectionate banter. The sole memento Lewis has of his parents is a magic 8-ball, an item he cherishes deeply.

That first night, as Lewis attempts to settle down, he is disturbed by an unsettling ticking noise and witnesses Jonathan frantically searching for its source. His first day at school introduces him to Tarby Corrigan ([Sunny Suljic]), who feigns friendship solely to secure votes for class president. Teased by his peers for wearing goggles, a tribute to his beloved TV hero, Captain Midnight, Lewis struggles to fit in. That night, he dreams of his mother, Mother ([Lorenza Izzo]), who warns him that Jonathan is hiding significant secrets, and that the ominous ticking is most definitely real. She advises Lewis to seek out a specific book followed by a key.

Driven by curiosity and fear, Lewis explores the dark corners of the house, discovering eerie dolls and Jonathan wielding an axe against a wall. Terrified, he flees, only to watch as household items such as the windows, a piano, and a peculiar “pet chair” named Chairy spring to life. Jonathan ultimately comes clean, explaining that magic is woven into the very fabric of their home. He reveals to Lewis that he is a magician, while Florence practices witchcraft. The home’s former owner, the malevolent Isaac Izard (Kyle MacLachlan), supposedly left behind a mystical clock, and Jonathan has been seeking it to uncover its purpose. At Lewis’s insistence, Jonathan begins to teach him the magic of warlocks.

In his lessons, Lewis learns that true warlock magic involves battling an evil spirit. Jonathan’s one uncompromising rule: never open the locked cabinet. While perusing an old scrapbook chronicling Isaac’s past as a renowned illusionist, Jonathan confides in Florence about his reluctance to reveal the complete truth to Lewis.

Preparing for Lewis’s first spell, Jonathan and Florence realize that for the incantations to succeed, Lewis must tap into his own unique form of magic. Following a night of intense training, Lewis learns why Jonathan left home; he always felt like the “black swan” in the family, rejected for his affinity for magic, especially because his father disapproved.

Unfazed, Lewis continues honing his magic, even at school, where he catches the attention of a girl named Rose Rita Pottinger (Vanessa Anne Williams). When Jonathan discovers an old photo of Isaac and his wife Selena standing by an unusually armed gnome statue, it leads him to uncover blueprints that could unlock the mystery of the clock. However, Lewis suffers another blow when Tarby wins the class presidency and abruptly cuts ties with Lewis, dismissing him as just a “weird kid.”

As the plot thickens, Isaac’s ominous presence casts a shadow over their lives. In a dream, Mrs. Barnavelt warns Lewis about Tarby hindering their friendship. Encouraged with the notion of friendship, Lewis attempts a dubious spell to make Tarby curious about his magic. Intrigued yet fearful, the duo stumbles upon an ancient tomb, where Lewis unwittingly resurrects Isaac.

Now aware of the revived spirit, Jonathan and Florence scramble to protect their magic while devising a plan against Isaac. To shield their home, they adopt desperate measures, harnessing their magic against the impending terror. Lewis, struggling with overwhelming guilt from his actions, confides in Jonathan, who reluctantly sends Lewis off to stay with Florence for protection.

In her home, Lewis glimpses past memories of Isaac and Jonathan, enjoying joyous times before the war altered their fates. Florence reveals that Isaac’s dark magic came at a steep price, hinting at personal loss and grief that has hindered her magical abilities. After warnings go unheeded, a series of frightening events forces Lewis, Jonathan, and Florence to confront the malevolent forces now unleashed in New Zebedee.

In a harrowing turn, Lewis’ attempts to make amends lead them back to Isaac. Time begins to unravel, aging townsfolk as Lewis battles his demons within. As the lunar eclipse approaches, he must confront his fears, letting go of his past to reclaim his power and thwart Isaac’s catastrophic plan.

With courage at his side, Lewis discovers the location of the clock. A fierce battle ensues where Jonathan and Florence face Isaac and Selena, regaining control over their magic and ultimately restoring peace. Recognizing his own strength, Lewis becomes the hero, dispelling Isaac and Selena into oblivion as he embraces Florarose’s offer of family.

Now back at school, armed with newfound confidence, Lewis showcases a touch of his magical prowess during a confrontation with Tarby, solidifying his importance among peers. Together, Jonathan, Florence, and Lewis return home—united as a family, ready to tackle any challenges ahead.