Lewis Barnavelt, recently an orphan, moves to the town of New Zebedee, Michigan, to live with his mysterious uncle Jonathan Barnavelt. Lewis' uncle turns out to be a mediocre, though well-intentioned, warlock. His next-door neighbor and good friend, Florence Zimmermann, is a far more powerful good witch. Jonathan's house was previously owned by Isaac and Selenna Izard, a sinister couple who had dedicated their lives to black magic, and plotted to bring about the end of the world. Before dying, Isaac constructed the eponymous clock that he hid somewhere inside the walls of the house, where it eternally ticks as it attempts to pull the world into a magical alignment, which would destroy the world.
Lewis befriends a local boy named Tarby Corrigan, who is everything he is not—popular, athletic, thin—but the two soon begin to drift apart. Lewis tries to win Tarby back by demonstrating how to raise the dead in the local cemetery on Halloween but in doing so unwittingly releases Selena Izard from her tomb.
An escalating series of encounters with the sorceress' ghost builds to a final confrontation in the basement of Jonathan's house, where Lewis must summon up his courage and prevent the couple from finishing their work and bringing about the end time.
