The story follows 10-year-old Lewis (Owen Vaccaro), who moves with his uncle Jonathan Barnavelt (Jack Black) into an ancient house that has a mysterious ticking clock heart within its walls. After coming across several secret passageways, young Lewis learns that his uncle is actually a warlock.

He eventually finds a book of his uncle's spells, and unwittingly awakens an evil wizard, which sets in motion a chain of events tied to the clock/heart that is designed for doomsday purposes.