While the Librarians are attempting to retrieve one of the artifacts that vanished from the Library, the Eye of Zarathustra, they run into Flynn Carsen, who is also seeking the Eye. It turns out to be a trap, and Flynn is kidnapped and the Eye taken.
Flynn finds himself on a road trip with a mysterious amnesiac, Ray, who he eventually figures out is the spirit of the Library itself. Ray was ripped out of the Library and has been responsible for the missing artifacts. Without Ray, the Library is dying.
Eve joins up with the villainous Moriarty to track Flynn and Ray while the other Librarians work with Jenkins to stave off the Library's imminent demise. Eve and Moriarty catch up with Flynn and Ray just in time for Ray to take up the Staff of Zarathustra, which restores his missing memories.
With Moriarty's assistance, Ray is restored. Moriarty takes the staff and leaves, though he does assure Eve that he would be more than happy to backstab Prospero, if given the opportunity.
Ray is returned to the Library just in the nick of time, and he gives Flynn a few parting words of advice before being absorbed back into the Library itself. Flynn leaves once more to continue his quest to defeat Prospero.