Following his grandfather’s death, Jacob cycles through offices and hospitals as his parents try to figure out what is wrong with him. He has recurring nightmares about the monster he saw, and eventually he stops leaving the house, believing this is the only place he is safe. He blames himself for what happened, wishing he had believed his grandfather about the monsters. Everyone thinks he is insane, including the police, because he keeps talking about the monster he saw—however, he knows it was real.
Even Ricky does not believe him, swearing he did not see any creature. The two get into a big fight, which appears to end their friendship. The police conclude that a pack of wild dogs killed Grandpa Portman. Jacob’s parents send him to a psychiatrist, Dr. Golan, who convinces him that the creature he saw was a product of his imagination, a result of the trauma of his grandfather’s death. He still suffers nightmares, and Dr. Golan keeps writing him prescriptions. The medication makes him out of shape and miserable.
Dr. Golan asks if Jacob has any ideas what his grandfather’s last words might mean. Jacob has tried to figure it out with no luck. His parents decide to sell his grandfather’s house. He is enlisted to help clear it out, but his father becomes angered when he wants to keep all of Grandpa Portman’s old things. He locks himself in his grandfather’s bedroom, and that’s where he finds a box full of photos of the peculiar children Grandpa Portman used to talk about. They look so obviously fake that Jacob is sure his grandfather’s last words meant nothing.
His parents throw him a surprise sixteenth birthday party, much to his dismay. Ricky shows up, and the two pretend to be friends again for a while. He opens presents, and his Aunt Suzie gives him one from his grandfather. It is the collected works of Ralph Waldo Emerson, with Jacob’s name written in the cover.
Inside it, he finds the letter his grandfather meant him to read. It is addressed to his grandfather with the affectionate nickname “Abe,” from “Headmistress Alma Lefay Peregrine,” telling him everyone on the island misses him and wants him to send a recent picture of himself. He puts two and two together and realizes that Headmistress Peregrine is “the bird” his grandfather wanted him to find, since a peregrine is a kind of hawk. He knows he needs to go to this island in Wales and try to find her.
He convinces his parents to let him spend three weeks in Cairnholm, Wales that summer to look into his grandfather’s past, primarily because his father is a bird watcher and will accompany him to research the bird species on the island for a new book he hopes to write. In preparation for the trip, he attempts to call the only phone on the whole island, but is met only with an angry voice shouting, “Piss hole!”
They finally make their way to Wales. On the ferry ride to the island, the ferryman tells them about all the shipwrecks in the area, sunk by German U-Boats during the war. When they reach the little town, a local points them to Priest Hole, the one place with rooms to rent on the island. He also warns them against going out to the old abandoned children’s home alone.
They devote the next day to scouting out the island, but when his father wants to stop for a while at a particular spot to watch birds, Jacob goes back to town to find someone to take him to the abandoned house. He asks Kev, the owner of Priest Hole, and Kev sends the fishmonger, Dylan, with him, along with his friend Worm. They trick him by pretending that a shed full of animal dung is the house, and then refuse to go any farther, leaving him to continue on alone.
Jacob finds the house, an abandoned, eerie wasteland of a place. He hopes he will find Miss Peregrine still there, but doubts it. He explores it, finding scattered, old children’s toys and dilapidated rooms, and realizes that it is impossible that anyone still lives there. He leaves the house feeling further than ever from the truth.
Chapter 2 is the first chapter that takes place fully in the “After” period of Jacob’s life, and he is more of a loner than ever. He is isolated from everyone around him because they all believe he is crazy, unwilling to listen to him and eager to close the case of Grandpa Portman’s death once and for all. His only friend, Ricky, pushes away from him, also reluctant to associate with Jacob while he is in this state. Completely alone now, Jacob has to focus all his energy on figuring out what his grandfather wanted him to know.
The aftermath of his therapy proves the power of the mind. Jacob is able to convince himself that he was imagining things and that there are no monsters after a session with Dr. Golan, even though he saw the creature in the woods with his own eyes. Everyone wants so much for him to believe it is not real that he is able to do it, at least for a little while.
His relationship with his parents, though never particularly strong, becomes even more strained in the wake of his grandfather’s death. His parents care very much about appearances, and put Jacob in therapy not because they care particularly about his mental state, but because they care about what others think about them and their “crazy” son. Jacob is also at odds with his father over his attachment to Grandpa Portman, likely because of the difference between Grandpa Portman’s relationship with his grandson versus with his own son.
In these chapters, another mysterious figure enters the story: Miss Peregrine. Right now, the letter is all Jacob has of her, but it is enough to send him looking for her in the flesh. If Miss Peregrine is alive, she will be able to speak when Grandpa Portman cannot. She is Jacob’s clue into his deceased grandfather’s past, so he is determined to find her.
Jacob begins his journey to Cairnholm in Chapter 3. Whenever a character travels to someplace new, it is a sure sign that he/she will undergo a transformation in some way. In a new place like Cairnholm, Jacob will be able to shed all of the burdens he carried back home and develop a new identity away from his past. He is free to become whoever he wants, and in the process of discovering the truth about his grandfather, he will undoubtedly change himself.
The abandoned children’s home itself is a physical representation of Jacob’s deceased grandfather. Just like Grandpa Portman, the house is full of secrets and stories it is no longer able to tell. The house has left clues, just like his grandfather, but right now Jacob is unable to find them. He must work harder to unravel the truth and learn what it is that both Grandpa Portman and this abandoned house wanted to tell him.