Jacob, Emma and Addison are stuck between a phone booth and a hollow. Jacob manages to control the monster and they escape but wights are after them. They pick up wounded Sergei, the folding man, and run. Jacob orders the hollow to attack wights. As they are running Jacob sees that the hollow is trailing after them.
Running from wights Addison picks up the trail of Miss Wren and it leads them to a boat harbour where they meet a boatman Sharon. They manage to talk him into leading them to the loop called Devil's Acre where their friends are most likely kept. He does and upon arriving there Jacob sees how diseased and decayed the place looks-like a hell hole.
Rowing in the boat they get stopped by a group of locals and Jacob realises that the hollow is under their boat. He orders the hollow to attack the men. The hollow appears to have killed itself along with the vultures.
They get on shore and persuade reluctant Sharon to help them. He leads them into the heart of the place and it appears to be different from what they've seen so far: clean and orderly.
Sharon leaves the peculiar trio and they find a lead to the wights' fortress where their friends are kept. As they arrive there they realise they can't get through; there is a hollow under the bridge leading to the place and the bridge is not finished. A prison car arrives and corrupted peculiars addicted to Ambrose that are surrounding the area attack the wights from the car for more substance. After the car leaves they turn their attention to Jacob and Emma and start beating them. Sharon and his riggers come to the rescue. Addison attaches himself to the wights' car and crosses the bridge.
Jacob wakes up in Mr Bentham's house. The man is Miss Peregrine's and Caul's brother. He tells Jacob and Emma the way of getting their friends back. It requires a hollow to turn on his house, which is actually a machine made for interloop traveling called Panloopticon. He also tells them about the Library of Souls, a place where peculiar souls are kept and the one who gets to control it can control the entire peculiardom. It requires twelve ymbrynes and the librarian to be able to use the souls and that is what Caul is after.
Jacob, Emma and Sharon set out to capture Jacob's hollow-the monster didn't die before, instead the locals captured it. Jacob is now in full control of the hollow and he takes it out of captivity and they bring it to Bentham's house.
Bentham powers his machine with it and Jacob and Emma cross over to Caul's Panloopticon. There they find their friends and ymbrynes captured. Jacob gains control over all of the hollows captured in the wights' fortress and a battle between peculiars and wights begins.
Just as they think they won Bentham betrays them and Caul leads them all to Abaton-the loop where the Library of Souls is stationed.
Finding what he looked for Caul takes one of the souls and turns into a peculiar giant. Bentham gives Miss Peregrine instructions to destroy the Abaton loop and he turns into a giant as well. The brothers face off while the ymbrynes are working on destroying the loop. Peculiars and ymbrynes all escape the loop and the wights' tower gets destroyed together with its owner and the Abaton loop. The battle against wights is finished and peculiardom is safe.
Jacob decides to return home and he and Emma promise to write each other letters.
Back home Jacob puts on a perfect show but his parents discover Emma's letters. He is about to be taken to the mental hospital but Miss Peregrine and peculiar children come to his rescue. They discovered that their age has been reset and that they won't age forward and they decide to take vacation in Jacob's home.
