The story picks up immediately after the events of the previous book previous book. Jacob Portman and his peculiar friends find themselves fleeing the safety of their loop after a group of wights disguised as Nazis destroy it. The children are in rowboats trying to reach Wales. A storm hits during the journey. Everyone manages to survive, but they lose almost all their supplies. On land, they soon realize that the wights that attacked their loop aren’t the only ones after them. The group takes to the woods where they run until they are too tired and stop for the night.
In the morning, they discover a lake with a human-shaped rock. Emma, a girl who can make fire with her hands, recognizes the place from the Tales of the Peculiar and goes to investigate. She discovers an entrance to another loop and leads Jacob and the others through. In the loop, Jacob senses hollowgasts and leads the group to a pulley system with a sign saying it’s the entrance to a menagerie.
With the help of Olive, a girl lighter than air, and the pulleys, the group makes it to the top of the cliff and out of a hollow’s grasp. Jacob directs Bronwyn, an unusually strong girl, to throw a boulder on the hollow, which kills it. Now safe, the children venture to the menagerie and meet Addison, a talking dog, and a number of other peculiar animals, such as chickens that lay exploding eggs.
Addison agrees to help the children as best he can. He examines Miss Peregrine, who has been stuck in bird form. He tells the children that only another ymbryne — a woman who can turn into a bird and control time — can help her become human again; if she stays a bird too long, she will become stuck in that form. Addison informs the children that his ymbryne, Miss Wren, traveled to London to try and help her sisters, who she believe were being kept in punishment loops by the wights. Armed with this information and the knowledge that Miss Peregrine’s time is running out, the group, led by Emma and Jacob, leave the loop with London as their final destination.
The children come across a gypsy caravan and secretly climb onto the back of a wagon. Eventually they are discovered, but before the gypsies can decide what to do with them, a group of wights who are searching for the children arrive. Recognizing the children are peculiar, the gypsies hide them from the wights.
The gypsy leader, Bekhir, agrees to bring them to the train station in the morning so they can catch the first train to London. At the station, the children try to board with Miss Peregrine still in bird form. A train conductor tells them that animals aren’t allowed, so they pretend that Miss Peregrine is a lifelike windup toy. Not fully convinced, the conductor makes them put Miss Peregrine in a trunk.
The trunk makes it onto the train, but the group is stopped when a wight dressed as a British soldier arrives and takes the children hostage. In the chaos, Hugh, a boy with bees living inside him, slips away. Jacob and the rest are marched away from the train station and to a nearby house, where wights hold Bekhir and the gypsies who helped them captive.
Mr. White, the leader of the wights, threatens to kill the gypsies unless the children reveal where Miss Peregrine is. The interrogation grows dangerous, but suddenly insects from the field outside swarm the building and kill the wights. When the insects disperse, Jacob and the others find that Hugh convinced the insects to save them.
The children quickly take the wights’ vehicle and drive to the next train station, where they catch the train to London and find Miss Peregrine unharmed. When they arrive in London, the group remembers that Addison said Miss Wren used peculiar pigeons as messengers and spies. Following a hunch and a story from the Tales, they head to St. Paul’s Cathedral to try and find the peculiar pigeons.
The search leads them to the catacombs below the cathedral, where they meet Peter and Joel, two blind boys who use echolocation to see. They reveal that the catacomb is an entrance to their loop, which was invaded by hollows. Only Jacob, Emma and Horace enter the loop, hoping to catch a pigeon.
Inside they meet Melina, who has the power of telekinesis. She has one of Miss Wren’s pigeons and insists on going where the pigeon goes. Jacob senses the hollows in the loop getting closer, so the children flee. The wights follow them into the catacombs, and the group must find a place to hide.
They take shelter in a nearby house with Sam and Esme, two young girls who stayed in London rather than be evacuated to the country. The children wait until an air raid siren begins to frighten Esme. Enoch, a boy who can animate the dead, uses his powers to make a clay figure come to life to distract Esme.
Using his abilities alerts the hollows to the peculiar’s whereabouts. The children flee just before a German bomb falls on the house, killing the hollows and impaling Sam with debris. Emma thinks Sam is dead, but it turns out that she is a peculiar and simply has a hole in her chest, which she says will go away. Sam and Esme part ways with Jacob and his friends.
Without the threat from hollows, the children’s search for Miss Wren continues. Melina’s pigeon helps them find another loop. The group ends up at a carnival. Figuring the sideshow performers might be peculiar, they begin asking them if they know Miss Wren. Eventually a carnival worker tells them that the real show is down the road. Following his directions, the children see a building that appears as though ice exploded out of it. A woman outside the building reveals herself to be Miss Wren, and she leads the children inside through a hidden passage.
A number of the sideshow workers are in the building and reveal that they are trying to form a peculiar army. They show Jacob and other peculiars that have been tortured by the wights, almost to the point of insanity, hoping the revelation will convince them to join the fight. The children are torn about whether to fight or to wait until Miss Peregrine is back to her normal self and can advise them.
Once alone with Jacob, Emma tells him to go back to his own time because he has a family and a future waiting for him. Eventually Jacob agrees to go. Jacob tells the others about his decision, and though they will miss him, they know it’s for the best. Before he leaves, Emma lets Jacob watch Miss Wren help Miss Peregrine become a human again. When the bird turns human, it isn’t Miss Peregrine but her brother, Caul, who is a wight.
After killing the peculiar girl who created the ice fortress that protected them, Caul takes them and the sideshow workers captive. The wights march their captives out of the loop and into a present-day London subway station. The peculiars fight back, and in the chaos, Addison saves Emma and Jacob by pulling them into a phone booth to hide.
Hollowgasts sense them and begin to attack the phone booth. Jacob finally gives in to his peculiar gifts, wholly; when he gives the hollow a command, it obeys. The day is saved. Eventually Jacob speaks to his father on the phone and tells him that he isn’t crazy; he’s peculiar.