The group of peculiar children which includes Jacob-the boy who can see hollows, Emma-the girl who can make fire with her hands, Bronwyn-an unusually strong girl, Olive-girl lighter than air, Hugh-boy who has bees in his stomach, Enoch-a boy who can bring the dead to life, Horace-boy who has dreams of things to come, Fiona-a girl who can make plants grow, Millard-an invisible boy, Claire-a girl with extra mouth on the back of her head is rowing in boats in order to escape from the wights. They finally reach the island, exhausted, but they can't rest for a long time as they soon find out that there are wights in air balloons searching for them.
They find a hiding place and as the morning comes discover another loop with the help of a book called Tales of the Peculiar. The loop is that of menageries-peculiar animals and on the way to their hiding place the peculiar children kill a hollow. They manage to kill it because of Jacob; he is now not only able to see the hollows but also to predict their next moves.
They meet a peculiar dog named Addison and he shows them the way and means to get to London to help the peculiar children's headmistress ymbryne Miss Peregrine heal and turn human again.
On the way to the train station the peculiar group meets a group of traveling gypsies. They have their misunderstandings but they discover that there are peculiars among gypsies as well and gypsies help them reach the train station.
On the train station just as they are about to depart a group of wights capture them and bring them to a small house on a field. The wights haven't captured Hugh and he helps the peculiar group escape.
When they finally reach London they are met with a war stricken zone, there are bombs falling and debris everywhere. Again with the help of the Tales of the Peculiar they find out that they have to locate Miss Wren's peculiar pigeons and find Miss Wren in order to help Miss Peregrine. The pigeons hiding place is the St. Paul's cathedral and they discover another loop there. In the loop they meet more peculiars and discover one of Miss Wren's pigeons.
Hunted by hollows they leave that loop and find a hiding place in one of seemingly abandoned houses. In that house the peculiar children meet with another peculiar girl called Sam and her normal sister. They don't part with Sam on good terms as she doesn't want to go with them because she can't leave her sister behind.
Following Miss Wren's pigeon the group enters a tourist loop and attend a carnival there in hopes of finding Miss Wren. Hopeless, they reach a house where all of the ymbrynes meet. The house is completely frozen and in the crowd of people they finally discover Miss Wren.
Miss Wren leads the group into the frozen fortress, which is her and other peculiars hiding place. She promises to bring Miss Peregrine back to normal. Emma urges Jacob to go back home after everything is finished. In the frozen fortress Jacob discovers a half frozen hollow barely alive. He decides not to kill it.
Miss Wren has finally succeeded to make Miss Peregrine turn human again. As the bird turns human the group realizes that it is not Miss Peregrine but a man, Caul-Miss Peregrine's brother. Caul kills the girl who made the frozen fortress and the ice melts fast. The peculiar group and Miss Wren are captured.
The soldiers bring them through the loop to the present time. Emma and Jacob manage to get loose from the soldiers and chains holding them and Addison helps them hide. Jacob watches as his friends are being taken away.
Jacob's phone rings and he answers to hear his father on the other line. Suddenly, the hollow from the frozen fortress is right in front of them. Just as the hollow is about to kill him Jacob is able to tell it to back off. He says to his father that he is like his grandfather, that he is a peculiar and then hangs up. Jacob orders the hollow to stand and the monster is obedient to him like a shadow.
