This book begins exactly where we left off in book one, with the children going to try to find another ymbryne which hasn't been captured yet so they can try to get Mrs. Peregrine back to her human form.
They are traveling on their boat away from their loop and make it to shore.
They find another loop and enter it to discover talking animals, another type of peculiar. They found this loop by using their fairy tale book that Mrs. Peregrine used to read to them from. It turns out that a lot of the things in the tales are true, since when they see a large stone giant in the middle of the lake which is in one of the tales, they find out it's a loop entrance.
The dog, Addison, who is pretty much the leader of these peculiars since their ymbryne has left for London to try to help her fellow ymbryne's, tells them that their ymbryne can help Mrs. Peregrine but that they must hurry because after a while she will become only a bird and hold none of her former self.
They hurry off to London but are captured by first gypsies, and then wights in the process. They escape by Hugh making his swarm of bees kill the wights. The gypsies turn out to be peculiars also who help them escape. The leader asks the children to take his son with them, who is much like Millard in that he is beginning to become invisible, but the children tell them that the boy will be better off with his family for now since they are on a dangerous mission.
They make it to London and try to find the ymbryne. They read from the tales again to try to get a clue, which leads them to believe they should track some pigeons which are actually an ymbryne's birds. They are led by these pigeons into a crypt where they discover another loop and more peculiar children, one who is a telekinetic, and a set of twins who are blind but use echolocation to find their way around.
Hollows come through the loop after the kids (although hollows should not be allowed to enter loops so this is a new development) and they all escape by running outside and into another building where 2 young girls who are sisters are also hiding. While the bombs are falling (they are now back in their own loop during the war), one of the sisters is punctured through the chest by a large beam that falls but she says it doesn't hurt.
She is actually a peculiar who doesn't bleed or feel pain, and while they have been hiding together the children have grown to really like these 2 girls. They ask her to come with them but she says she can't, that someone tried to come get her once before but she won't leave her sister behind since her sister is normal and can't enter the loop.
The children find that when the bomb dropped and destoyed the building, their sweaters protected them and are a type of enchanted armor. Bronwyn, the strong girl, gives her sweater to the girl's young sister to protect her before they leave.
The telekinetic girl is friends with one of the magical pigeons and goes with them so the pigeon will follow and they can try to find the loop they need to find the ymbryne. They are all very distraught when Miss Peregrine, while interrogating the bird as a bird herself, kills the pigeon after getting the information they need.
They enter the loop and come into a carnival of sorts. While looking for the ymbryne within the carnival they see a man who can bend himself crazily, a creepy clown, and a woman with a large python she can control with just her voice and touch. These people also turn out to be peculiar as well though they deny it when the children ask them.
A boy gives them a hint on where to go, and they head to the street he mentioned. When they arrive they see the place is frozen over, but the ymbryne finds them and takes them inside. They meet another peculiar girl here who the ymbryne introduces as someone who can freeze upon touch and she had her freeze this place so the hollows and wights couldn't get them.
The ymbryne takes Mrs Peregrine to try to heal her and the children begin conversing with the people from the carnival who are at this building now. They tell them they want them to join the fight against the hollows to get the ymbryne's back but the children say no, that they just want Mrs Peregrine back and to go home.
The carnival peculiars then show the kids a room full of fellow peculiars who are lying in beds with vacant stares in a hospital wing, and tell them that no matter where Mrs Peregrine takes them they won't be safe because the wights and hollows have figured out how to steal children's souls, hence why they can now enter loops.
They further tell the kids that the reason the ymbryne's have been kidnapped is because the hollows and wights are trying to use the ymbryne's to become whole again and take over the human world and all loops.
The kids make the decision to fight back but Emma, the firestarter and Jacob's love interest, tells Jacob she wants him to go home after this is all over while he still has a loop to travel through to get back to his family. He argues but eventually agrees since it's what Emma wants.
The ymbryne gathers them all back into her chamber to wait while Mrs Peregrine turns back into herself, but it's actually Mrs Peregrine's brother who emerges from the bird. Turns out when they kidnapped Mrs Peregrine back from the wights in the first book it wasn't her at all, but him disguised as Mrs. Peregrine.
He tells them he has alerted the wights and hollows of their location and they come in and capture the children and other ymbryne. This was his plan all along; for the children to lead him to this ymbryne who was so well hidden.
Emma and Jacob escape while they are all being loaded onto a subway train but a hollow attacks them inside a phone booth. Jacob calls upon the power in himself and is able to control the hollow by talking to it in his thoughts. The book ends with all the rest of the children captured, Jacob and Emma and now a "pet" hollow going after them to rescue them and the ymbrynes.
Sorry if I made any mistakes in this. Feel free to correct me if so, since it's been a couple weeks since I read this.