Apep, the Egyptian God of Chaos, is revived, and attempts to release Pure Evil into the world, beginning the ultimate battle between good and evil. In order to do so, he kidnaps Charlene and forces Flynn to look for her.
Meanwhile, a new secret government agency, called D.O.S.A. (Department of Statistical Anomalies) has started investigating magic. Being normal humans, they are not aware of the existence of the Library, and as such blame the Librarians for all magic-related trouble they face.