After his grandfather's murder, apparently by a make-believe creature, 16-year-old Jacob Portman goes to Wales to learn the truth about his grandfather's past. He finds that his grandfather lived in a derelict orphanage for "peculiar children". That is where he meets Emma, a "strikingly pretty" girl who can control fire. She uses time travel to take him back to 1940 to meet Miss Peregrine, the orphanage director, who lives with the other children in a "time loop". Jacob enjoys spending time with the other peculiar children, such as Millard, who is invisible, and Bronwyn, who has incredible strength. In the pub where Jacob is staying, he hears stories of mysterious deaths in the region, and he warns the peculiar children. They tell Jacob that the deaths were caused by the "hollows" or "hollowgasts", the same monsters that killed his grandfather. Jacob later learns that he too is a peculiar, and realizes only he can see the monsters and stop the killings.
After Jacob (with Emma's help) kills one of the hollows, Miss Peregrine is kidnapped. The children rescue Miss Peregrine, but she is in bird form and cannot change back to human form. Ultimately the peculiar children must find another time loop when theirs fails to reset. A loop must be reset every day by the owner-in this case, Ms. Peregrine-and she is trapped as a bird, causing the loop to disappear and forcing the children to find a new home.