Jacob and Noor (the newly found peculiar who can eat light) are on the run from Leo Burnham’s gang in Chinatown, NYC. Leo runs the Northern Gang of American peculiars. Jacob and Noor escape and find their way to the Devil’s Acre loop where their friends are. Jacob was worried they’d be angry at him and he’d lose their friendship, but all is forgiven. Jacob explains that before H died he said to find V, who raised Noor. It also turns out the Noor is eluded to in a prophecy about 7 peculiars who will emancipate the peculiar world. No one really knows what this means. Noor has very little memory of her childhood, so Horace, Millard and the gang set up for the libraries to use what little clues they have to try to locate V, and to figure out the meaning of the prophecy. Hugh is upset that they’re trying harder to find V than they ever tried to find Fiona, who disappeared a couple books ago.
Miss Peregrine and the other ymbrynes are heading to American for the peace conference, to help settle things among the American groups. The night they leave, the wights escape from prison. Jacob has a bad feeling this is somehow connected to Miss P’s brother Caul, who is supposedly trapped in a collapsed loop, never to escape. It turns out Jacob, Horace and Miss P have all had nightmares or just bad vibes about Caul lately.
The ymbrynes return, but they need Jacob to join them; they need his hollowgast-finding ability. A Northern Clan girl has been kidnapped, and they think the Californios did it; it retaliation, they’ve taken a Californio. After a false start, Jacob manages to track down a hollow, and after a big chase, finds the kidnapped girl, and also finds clues that the wights who took her may also have Fiona. Somewhere in here, Miss P and the gang have deciphered more of the prophecy, and gather that the wights, led by Murnau, are gathering materials needed to…make bad things happen. Clues in the prophecy lead the team back to America, where they are able to track the wights. The good news is, they find Fiona. The bad news is, she’s in bad shape–the wights have taken her tongue, one of the objects mentioned in the prophecy.
Everyone gets back to Devil’s Acre. They believe that one of the objects is Miss Peregrine herself, and since she is safe, all is well. Fiona with Hugh by her side is off to the clinic.
Noor gets a postcard from V, from a small town in Pennsylvania. She and Jacob had there, and discover a loop that is one big tornado. Using a childhood rhyme that V taught Noor years ago, they manage to stay safe from tornadoes, and track down V, who is shocked to see them. It turns out she didn’t send the card, it was a trick set up the wight Murnau. And the object he’s after isn’t Miss P, it’s V! He kills(?) her just as Jacob loses consciousness.
In a little epilogue, some randome girl with a stuffed animal named Pensevus (who whispers to her) makes a 6 phone calls, saying only “He’s back.”