When Jacob Portman was young, he admired his Grandpa Abe (Grandpa Portman). His grandpa grew up in an orphanage, fought in WWII, and even performed in a circus! Grandpa Portman told Jacob weird stories and showed him photos of peculiar children including invisible boys, substantially brave girls, and people with mouths in the back of their heads. Eventually, he stopped believing these strange stories.
When Jacob was fifteen, his grandfather started yelling about monsters coming to eat him. Jacob and his dad wrote it off as dementia. After a little while, he checked on Grandpa Portman and found him dead. Jacob came face to face—well, face to tentacle—with the monster that killed him.
No one believed that a monster killed Grandpa. (Official cause of death: rabid dogs.) Jacob started having nightmares and slipped into a deep depression. His psychiatrist, Dr. Golan, suggested he went to the island where Grandpa was raised, the Cairnholm Island.
Jacob and his dad flew to Cairnholm Island in Wales, and Jacob found Miss Peregrine's home way out past the island's bogs. Snooping around the decaying estate, Jacob found a load of old photos like the ones Grandpa had.
Grandpa Abe was raised here, but Miss Peregrine (who can turn into a peregrine) old Jacob that he left to fight the hollowgast, the evil monsters that hunt the peculiars, and the same type of monster who killed Grandpa Abe. To stay safe from the hollowgast, Miss Peregrine created the time loop. They repeat the same day every day, and the bomb that falls on the house never explodes.
The hollowgast launched a plot to kidnap Miss Peregrine and other ymbrynes—shape-shifting women who can control time—to try the immortality thing again. Jacob's psychiatrist, Dr. Golan, turned out to be a wight, and Jacob lead him right to Miss Peregrine. Golan birdnapped Peregrine and her mentor, Miss Avocet, and carries them out to sea.
Jacob and his new peculiar friends gave chase, killed Golan and the hollowgast, and rescued Miss Peregrine. Miss Avocet was taken away, and Miss Peregrine was stuck in bird form. Because she couldn't change back, the time loop collapsed, the bomb fell, and the home was destroyed.
One of the children by Jacob said that they must go back in time to fix this time loop. She wrote a letter to Jacob's dad telling him the Jacob might never come back and time travels back to 1940, trying to fix everything that happened.