The team returns to the Library after the incident in New York and split up to investigate ways to beat Prospero. Jenkins is frustrated by mysteriously vanishing artifacts. Flynn and Eve head off to John Dee's old house to try to locate parts to Prospero's broken staff.
Jenkins is in the Reading room when he discovers that Prospero and Moriarty have breached the Library. Prospero wants to make a new, more powerful staff from the Tree of Knowledge at the Heart of the Library.
Flynn and Eve discover that someone, possibly an earlier Librarian, had already beaten them to the staff. They return to the Library, where the other Librarians are dealing with the lockdown that Jenkins initiated. They find Jenkins and learn of Prospero's plan.
They come up with a way to find the Heart of the Library themselves, but they are forced to deal with a couple other fictionals, the Red Queen and Frankenstein's monster. After handling both foes, Flynn and Eve find themselves in the Heart of the Library.
After a confrontation, Flynn apparently burns the Tree of Knowledge with an artifact, and Prospero leaves in frustration. After Prospero is gone, Flynn reveals that he'd tricked Prospero and had burnt a completely different and probably very important tree.
Flynn and Eve argue about their different styles of doing things, and Flynn leaves on his own to track down the missing artifacts while Eve remains with the other Librarians, once again united in common purpose.