The story follows a teenager named Jacob Portman, who is left reeling after a horrific family tragedy that appears to be linked to his grandfather's mysterious past. Haunted by his grandfather's tales of a magical place sheltering children with extraordinary abilities, and by his last cryptic words hinting at a hidden truth, Jacob decides to travel to Wales in search of answers. There, he stumbles upon the ruins of what was once Miss Peregrine’s Home for Peculiar Children. As he explores the abandoned bedrooms and hallways, he realizes that the children, considered peculiar by the outside world, were more than just unique; they possessed powers that defied reason and time itself.

Through a turn of events, Jacob discovers that these children are not just stories from the past; they live in a time loop, reliving the same day in the 1940s under the protective care of Miss Peregrine, who, like her charges, has her own peculiar abilities. As he gets to know the residents—among them Emma, a girl who can manipulate fire, and Millard, an invisible boy—Jacob learns of the danger that threatens their very existence. Sinister creatures led by a malevolent force are hunting the peculiars, prompting Jacob to realize that he too may have his own place in this unusual world. His life takes on a new purpose: to help protect the children and uncover the depth of his own grandfather's legacy.