In 1955, ten-year-old Lewis Barnavelt (Owen Vaccaro) goes to New Zebedee, Michigan to live with his uncle Jonathan (Jack Black) after Lewis' parents are killed in a car crash. Upon arriving at Jonathan's home, Lewis meets Jonathan's neighbor and best friend, Florence Zimmerman (Cate Blanchett), with whom he trades playful insults. All Lewis has left of his parents is a Magic 8-Ball that they gave him before the crash.Lewis tries to sleep that night, only to be kept up by what sounds like a faint ticking noise and notices Jonathan trying to find it. On his first day of his new school, he meets Tarby Corrigan (Sunny Suljic), who is being friendly with him just so he can get voted class president. The other kids think Lewis is weird for wearing goggles, which he based off his favorite TV hero, Captain Midnight. At night, Lewis thinks he is dreaming seeing his mother (Lorenza Izzo) who tells him that Jonathan is hiding something from him and that the ticking sound he hears is real. Mrs. Barnavelt also tells Lewis that he must find a book and then a key.Lewis then gets up and goes around the house in the dark and finds several creepy-looking dolls and Jonathan smashing a wall with an ax. Lewis runs away freaked out and sees the windows, piano, and a "pet chair" named Chairy among other things coming to life. Jonathan is then forced to explain himself and tell Lewis the truth about magic being involved in the house. He reveals to Lewis that he is a practicing warlock and that Florence is a witch. The house's previous owner is a sinister warlock named Isaac Izard (Kyle MacLachlan) and his equally wicked wife Selena (Renee Elise Goldsberry). Before Isaac died the previous year, he left a clock in the house and Jonathan has been trying to find it and discover what it is meant to do. At Lewis's request, Jonathan decides to teach him how to be a warlock.Lewis learns that, in order to be a legitimate warlock, he must fight an evil spirit using his own magic. Jonathan lets Lewis know that he has only one rule: never open a cabinet that he has locked.Jonathan looks through an old book with clippings of Isaac when he was a famous illusionist, as well of pictures of him during World War II. Jonathan reveals to Florence that he has not told Lewis everything about Isaac and plans on continuing to lie to the boy.Jonathan and Florence gets Lewis ready for his first ever spell. When he reads off the spells from the books, it doesn't work because they tell Lewis he needs to use his own brand of magic for it to work. After a night of learning magic, Lewis asks Jonathan why he left home. He says he considered himself the "black swan" of the family as his father did not agree with magic, so he left and he felt that Lewis' mother would not have wanted him at her funeral.Lewis continues to practice his magic, even at school, which is noticed by a curious girl named Rose Rita Pottinger (Vanessa Anne Williams). Jonathan later discovers an old picture of Isaac and Selena with a gnome statue in it that was missing an arm, but now has one built. Jonathan pulls on the arm, which opens up a secret entrance that leads him into a room where he finds the blueprints for the clock.Tarby wins class president and then stops acting like Lewis' friend. Lewis tries to invite him over to show him magic to keep him interested, but Tarby opens Jonathan's restricted cabinet. There, Lewis spots the book that his mother had mentioned to him, and Tarby takes it out to open the first page that has a spell for necromancy. Lewis takes the book back and puts it away, leading Tarby to go home and says Lewis is just a "weird kid".Jonathan and Florence look over the blueprints and they are both stumped on how to decipher it. She notices an omega symbol with a skull, which Isaac mentioned before he died. They also realize it was, in early Christianity, a symbol for Judgment Day.Lewis is once again visited by his mother in a dream. He laments that Tarby doesn't see him as a friend, so Mrs. Barnavelt suggests that he use a spell from the forbidden book to make Tarby want to be his friend. He invites Tarby to join him so that they can raise the dead. Later that night, Lewis and Tarby find a tomb and Lewis starts to read from the spell book. The tomb opens and Tarby runs away. Unknowingly, Lewis has just resurrected Isaac Izard.Jonathan and Florence realize that Isaac is back and all of their magic stopped working. They know their magic isn't strong enough to face him yet, so they start to nail horseshoes to the house to keep Isaac away. Lewis tries to confess what he did, but Jonathan and Florence vow to make the one who resurrected Isaac pay. Jonathan sends Lewis to stay with Florence for a few days.In Florence's home, Lewis notices a poster advertising Isaac and Jonathan as a magician duo. Florence shows Lewis a series of flashbacks that showed Isaac and Jonathan performing as magicians together until Isaac went MIA during World War II. Isaac later returned home, but was suffering from PTSD. He mentioned being in The Black Forest, which is known for harboring dark magic, and Florence thinks Isaac made a deal with a dark warlock there in exchange for the powers he later possessed. He also later married the spiteful and wicked Selena. Florence then explains how Isaac performed the dark magic ritual to make a key for the clock, which is believed to have been made from Selena's finger bone. When Lewis asks Florence why she can't help stop Isaac, she takes a look at a picture of her deceased husband and daughter. She states that because of her pain, she hasn't been able to work the same magic that she used to.When Lewis tries to warn Tarby about Isaac, Tarby punches him in the stomach and orders him to keep quiet or he'll break Lewis's arms. Lewis goes back home to find the blueprints so he can help out, but he is attacked by flying books. He gets out as Jonathan and Florence arrive to help him. He tells the two that he can read the blueprints, but he needs ovaltine. They go to a nearby candy store where Lewis uses a bunch of chocolate powder to try and decipher the markings on the blueprints. They soon discover that the clock is a doomsday device that will reverse time all the way to the beginning.The three return home to find the horseshoes have been pulled off the walls, meaning Isaac was there. They enter the house to find it ransacked. Jonathan and Florence decide to destroy the key, but it won't dissolve in the acid they dip it in. Lewis then confesses to resurrecting Isaac just to impress Tarby and also because he thought that if the spell worked, he could see his parents again. Feeling betrayed, Jonathan decides he wants to send Lewis away for disobeying him. Lewis runs away crying and Florence tells Jonathan that he is being a coward for trying to avoid responsibility for the boy.Lewis notices Issac in the house of Jonathan's neighbor Mrs. Hanchett (Colleen Camp). Lewis brings her to the house, but before Lewis can find Jonathan, Isaac emerges. He then reveals that Mrs. Hanchett is really Selena in disguise and that she killed the real Mrs. Hanchett, took her place, and that the key was made from her bones. Selena also reveals that she was taking the form of Mrs. Barnavelt to persuade Lewis into doing her bidding to bring Isaac back.Isaac captures Lewis, followed by Jonathan and Florence. He explains to them that because of the horrors he saw in the war, he wanted to completely forget what he saw. He met a demon named Azazel in The Black Forest and he granted Isaac the power to make his wish come true. Issac reveals that the clock will turn time back so that humanity never existed and uses the creepy dolls and killer pumpkins to send the three away.Jonathan apologizes to Lewis for how he talked to him and they all plan to go back and stop Isaac and Selena. Lewis uses the Magic 8-Ball to learn that the location of the clock is under the boiler room. Using all their wits and magic, the three go back to destroy the pumpkins and dolls to find the clock.Florence gets taken by Jonathan's mutated snake named Snakespeare, leaving Lewis and Jonathan to face the villains on their own. Isaac awaits as the lunar eclipse is setting, which will activate the clock's power. He and Selena are protected from the clock's effects. Lewis and Jonathan try to fight back, but Jonathan is morphed into a weird baby that still has his adult head. The eclipse happens, and people around town start to de-age to children. Lewis consults the Magic 8-Ball to know what to do and it says "Say goodbye". Lewis realizes he has to let go of his pain from losing his parents to harness his true power. He drops the ball into the clock's gears to slow it down, which makes Isaac and Selena leave their protected post. Using his own magic, Lewis zaps Isaac and Selena, causing them to fall, de-age, and ultimately be erased from existence. Everything goes back to normal as Florence reveals that she has fixed Snakespeare and Lewis offers her to be part of his new family.Lewis goes back to school with more confidence. Tarby and his friend refuse to pick Lewis for sports, so Lewis shows off a little bit of magic by making a basketball bounce off Tarby and his friend's faces to sink it into the net. Even though everyone now wants Lewis on their team, he instead hangs out with Rose Rita.Jonathan then picks him up from school where they go home with Florence as the three of them are now like a regular family.