Jacob only has a few more days to decide whether to leave his father and stay in the loop, or to go with him back to the US. His father has been wallowing and drinking heavily, sure that his new book is not going to work out, so it is easy for Jacob to sneak away into the loop. At the house, Miss Peregrine has instituted what is nearly a lockdown in order to keep everyone safe, and all of the children are stir-crazy. Miss Avocet is still there, and everyone speculates as to why the hollows would want to kidnap ymbrynes. Jacob sees Horace make an apocalyptic prediction one night.
Martin, the museum curator in Cairnholm, goes missing, and they later find his body in the ocean. Jacob's father discusses running into the strange other birdwatcher the other night, wearing sunglasses in the dark. Jacob fears that this means he is definitely a wight. There is a major storm about to hit the island, and Jacob is instructed not to leave Priest Hole, but he sneaks out so that he can warn Miss Peregrine about what he heard. Emma and Millard believe it was a hollow who killed Martin. Miss Peregrine says that no one is allowed to leave the house, not even Jacob. He puts up a fight because his father is stuck out there in town, but Miss Peregrine says if he chooses to leave he can never return.
Jacob decides to leave anyway to try and get the hollow before it gets them, and Emma, Bronwyn, and Enoch decide to sneak out of the loop with him. The plan is for Enoch to rouse Martin to ask him what killed him. They make it into town and go to the fishmonger's, where they are keeping Martin's body. Enoch rouses him with a sheep's heart, and he wakes up and recognizes Jacob. He says "my old man" killed him, and Jacob realizes he is talking about the bog boy that he saw in the museum when he first arrived on Cairnholm. He also realizes that Martin is mistaken—he thought he saw the bog boy, but it was really a hollowgast, visible to the common eye only when it is eating.
Suddenly the mysterious bird-watching man appears, and he knows about all of them. He lists their names in turn, even Jacob's, and then reveals that he has been present in Jacob's life in many ways for years and years. He was his old middle-school bus driver Mr. Barron, his family's lawn and pool cleaner, and worst of all, his psychiatrist Dr. Golan. This wight has been following Jacob around his entire life. He reveals the grotesque Malthus, his hollow, and says if Jacob helps them, he has nothing to fear from Malthus or his kind. When Jacob refuses, Dr. Golan disappears, leaving Malthus to eat them. They fight it and try to make an exit, and are eventually able to because Bronwyn uses her strength to beat him.
Enoch accuses Jacob of betraying them and allowing Dr. Golan to follow him straight to them. Bronwyn and Emma defend him. Afraid that Dr. Golan has figured out how to get into the loop on his own, they run towards the loop in the woods, with the hollowgast pursuing them. Bronwyn and Enoch run ahead while Emma and Jacob veer off to try and lead the hollow away. They hide in the shack full of sheep manure, and the sheep themselves are inside it sheltering from the rain. Jacob tells Emma that if they make it through this he is staying with her, but then the hollow enters the shack and begins to eat the sheep. They run and make it to the cairn, and Jacob buries garden shears in the hollow's eyes and watches it die.
They go into the loop and to the house, only to learn from Bronwyn and Enoch that the wight made it in and captured Miss Peregrine and Miss Avocet as birds and took them away. The kids are in chaos; Jacob says they have to do something, so they run to where the wight tried to escape the island in a boat. The tide got too rough, so Dr. Golan and the ymbrynes stopped on the lighthouse rock - and are still there. Emma, Bronwyn, Millard, and Jacob decide to swim across to them, but Dr. Golan begins to shoot. Millard gets shot and is badly injured. Bronwyn rips the metal door off the shipwreck they are sheltering in to use it as a shield to get Millard and the rest of the group to the lighthouse, which is the closest land.
At the lighthouse, Bronwyn hits Dr. Golan with the door and knocks the wind out of him, and Jacob and Emma pursue him while Bronwyn makes a tourniquet for Millard. They trap him at the top of the lighthouse, and he threatens to throw the cage with the ymbrynes in it over the side. He reveals that they need the ymbrynes to finish the experiment they started and become immortal. He throws the birdcage over into the ocean, and Jacob summons up the courage to pull the trigger and shoot Dr. Golan with his own gun. Once he is dead, they head out immediately to try and retrieve the birdcage from the ocean.
As they are pursuing the cage, a German U-Boat appears, manned by wights. One bird has escaped the cage—Miss Peregrine—but the wight takes Miss Avocet and the U-boat disappears. The group makes it back to shore with Miss Peregrine. Millard is badly injured, and they realize that the loop has not reset. Miss Peregrine is unable to turn back into a human. Because the loop did not reset, the house has been bombed and is in shambles. They realize the hollows and wights will soon come back for Miss Peregrine, and they know they need to pursue them and put a stop to their plan. Horace has a vision and draws a picture of where they are going, but it is vague and uninformative.
Emma locates something called the Map of Days, which is labeled with every loop ever known to exist. Millard explains to Jacob a concept called leapfrogging, where you travel to a loop and then have access to all other loops that existed at that time, even if they have ceased to exist in the present day. Through this method, you can travel through time. They are worried that the wights have taken the ymbrynes leapfrogging to a place that existed in the past, so they not only have to figure out where they are, but when too.
Jacob decides to abandon his former life and come with them to find them. He goes back to town in his own time and tries to explain to his father what happened. His father does not believe anything he says, and thinks Jacob is crazy until Jacob's friends appear. Emma shows them her flame hands, and Olive levitates, while Millard is invisible. Jacob tells his father he is going on a trip and will not be back for a while, and his father says he is just like his grandfather. He goes back to sleep, and they leave him a photo of Emma and Grandpa Portman as proof that the Emma he just saw was real. Emma also writes him a letter.
They go back to what had once been the loop—it is now September 4 for the first time. They bury Victor, and prepare three rowboats to set off and leave the island in. The ten children, with Miss Peregrine in her cage, set out on their next journey.
Jacob is given the choice to be part of the peculiar world, where he feels like he truly belongs, or to remain in the common world he has always known. The fact that this choice is difficult to make and that he considers the safety of his family shows that he has gained maturity over the course of this novel. He must choose between helping the people he has come to love in the loop and returning to the apparent comfort of his old life, leaving them to meet whatever fate befalls them. In the end, he makes the mature choice to help his friends who need him, while still ensuring that his father knows he is gone and will be okay on his own.
Miss Peregrine's role as a mother to her wards truly comes out in Chapter 10 as she attempts to secure the loop and ensure their safety. She puts the children of the house above everything else, and though she does care about Jacob, she will not allow him to jeopardize their safety. The chaos that ensues after Miss Peregrine disappears clearly shows that she was the glue that held the house together—however, she has also trained and guided these children well, and the way they rise to the occasion and try to rescue her rather than simply wallowing in sorrow shows that her fighting, determined spirit has made an impression on them.
Jacob is extremely perturbed to find out that this wight has been following him around his whole life. Things that were familiar—his bus driver, his neighbors—have now been corrupted, which is uncomfortable for him to think about. The knowledge that Dr. Golan was this wight all along is especially perturbing, since this is not only a betrayal of Jacob himself but of his mind. Dr. Golan messed with his mind and made him believe he was crazy, all for his own gain. When he learns this, Jacob realizes that not even his mind is safe from these monsters.
While Jacob certainly proves himself a hero when he kills Dr. Golan and leads the children to rescue the ymbrynes, he certainly does not do it all alone. The other children in the house all prove their worth and show that their abilities are not just peculiar, but also useful. They can use their skills for good, and they do. Bronwyn uses her strength to rescue them from the hollow, Emma uses her fire as a weapon against Dr. Golan, and Millard is even nearly killed attempting to use his invisibility to get them across the water. They are all heroes, and their effort as a team was essential in stopping Dr. Golan.
The loop's failure to reset is a symbolic loss of innocence for the peculiar children who lived in it. While inside the loop, they were able to hold onto their childhood both physically and emotionally, ignoring the outside world and under the constant protection of Miss Peregrine. The loop's failure means that Miss Peregrine can no longer protect them from the rest of the world, and they must grow up and face its evils, however awful they may be.
The theme of the fluidity of time continues as Jacob and the peculiar children realize what they must do in order to rescue the ymbrynes and stop the wights and hollows from destroying the world on their quest to become immortal. These different times—these loops—all exist at once, and the children must use their skills to move through all of these times and accomplish their mission. Time is powerful, but it can be manipulated by humans, so the children must counter-manipulate it to ensure that the natural order of things is not disrupted. It is a tall task, but one that they have proven themselves ready for.