It focuses on Jacob Portman, Emma Bloom, and Addison MacHenry trying to save their friends. Jacob and Emma meet a man named Myron Bentham, who is Alma LeFay Peregrine and Caul's brother. They learn that Jacob is more than he seems and is likely the final key to the Library of Peculiar Souls.
The novel begins when Jacob, Emma, and Addison are fighting off Hollows and Wights that have attacked Miss Wren’s secret hideout where dozens of peculiar children have taken refuge. The Hollows and Wights, under the command of the evil Caul, have kidnapped the peculiar children and many ymbrynes, mother-like protectors, guardians, and guides of the peculiar world. Among them is Miss Peregrine. Jacob, Emma, and Addison aspire to get them back. The cross into present-day London to chase Caul’s forces. Under the London docks, they meet Sharon, a boat man who agrees to take them into Peculiar London.
In Peculiar London is an area best by criminals of the worst kind, called Devil’s Acre. There, Jacob, Emma, and Addison try to figure out how to break into Caul’s fortress. Addison attempts to sneak in, but is captured. Jacob and Emma then meet Myron Bentham, an intelligent explorer and inventor who knew Jacob’s grandfather. Bentham reveals many startling things to Jacob and Emma. Among these are that he, Caul, and Miss Peregrine are siblings. Bentham also explains it was his fault that Hollowgasts and Wights exist at all.
Seeking power by feeding on the souls of peculiar children, Caul sought to find the legendary Library of Souls, where the souls of peculiars are kept and stored after death. They give the consumer immense power. Caul’s goal has always been to find the library and use it to take over the world. Bentham then sought to kill Caul and all his followers by closing the time loop they travel through, but only partially succeeds. In their place come Hollowgasts, essentially corpse-like versions of their former selves with no souls. When a Hollowgast has consumed enough peculiar souls, they are nearly restored to their former human state and become a Wight.
However, only a librarian can actually see the soul jars in the Library of Souls. Jacob’s grandfather was one such man. Bentham explains he and Jacob’s grandfather were experimenting with fracturing his grandfather’s soul to see if that particular power could be given to others rather than just being born with it. As a result, Jacob’s grandfather lost all his peculiar powers, and left the peculiar world. He was later hunted down and killed by a Hollowgast. Jacob now has the same librarian power, which is why Caul is seeking to capture him. Emma does not trust Bentham, thinking he took Jacob’s grandfather’s powers rather than his grandfather surrendering them voluntarily.
Nevertheless, Jacob and Emma rely on Bentham to use his home –a central point for loops –to get them inside Caul’s fortress in Devil’s Acre. Once there, Caul springs a trap on Jacob and Emma to capture them with Bentham’s help. Jacob, Emma, Miss Peregrine, Caul, Bentham, and a handful of Wights then venture through a loop to the Library of Souls in Abaton. They come across a throne room with a fountain and pool for the consumption of souls. Caul begins the process by transforming himself into a hideous, gigantic beast. Bentham, who is power-hungry but not evil, sacrifices himself by giving Miss Peregrine the spell to shut down the loop as Bentham did once before. He then transforms himself into a hideous monster by consuming souls and attacking Caul. Miss Peregrine and her fellow ymbrynes successfully shut down the loop, ending Caul’s reign of terror.
Afterwards, Jake decides to go home to his family, and tells them a bogus story about his getting amnesia and getting lost. They believe him, and aside from his continued seeing of a therapist, he's for the most part treated normally. He keeps up correspondence with Emma, and writes her back unlike his grandfather. She in turn keeps him informed about the children's whereabouts and doings. But one day, his parents find Emma's letters, and take them to the therapist, thinking he wrote them himself. The therapist recommends Jake be taken to an "in-patient clinic" for "monitoring and rehabilitation," and despite Jake's efforts to get out of it all seems lost.
But on the day they are about to leave, Miss Peregrine and her children show up, shocking Jake's parents and confusing Jake, thinking they're about to age forward. But Emma explains that Caul's loop collapsing reset everyone's internal clocks, so they will never age forward, and so can come live with Jake. As the children get settled and work on Jake's parents, Jake suggests to Emma that maybe he could teach her how to be normal, and Emma accepts, saying why not, because they had time.
The novel ends with Jake saying what he thinks are the best words in the English language: "We Have Time."