Jacob and his peculiar friends are reunited in Florida; they no longer have to worry about rapidly aging outside their loop.  During an outing, they discover the safe house and mission book of Jacob’s grandfather.  Jacob contacts his grandfather’s partner, H, who sends him on a mission.

Jacob, Emma (fire hands), Bronwyn (strong), Enoch (can raise the dead) and Millard (invisible) head off to rescue an “uncontacted” peculiar girl. They pass through Flamingo Manor (a loop in Georgia) and Portal (another loop).  They make friends in both places before heading to New York where they locate Noor, a girl who can “eat” light and make it completely dark, and also spit the light back out.  They are arrested by a gang led by a man named Leo, who wants to kill Jacob for the perceived crimes of his grandfather.

The group is rescued by Miss Peregrine, who is furious.  They have endangered the ymbrines peace talks to help settle things down in America, where peculiar society is made up of 3 rival gangs and many unorganized loops.  She also tells him about an old group of normals who have a been trying to eliminate peculiars for years. Jacob still think they were doing the right thing by trying to help Noor. Leaving the rest of his friends behind, he makes his way back to H, only to find him dying by the hands of the men who were hunting Noor.  Noor is also there.  H dies, and Jacob and Noor escape, to hunt for Jacob’s other partner, a woman known as V.