A mysterious man uses magic to summon a character from a copy of Sherlock Holmes.
Months later, the Librarians are all separate, operating independently of each other. They each get a summons to go to a museum exhibit in New York. Instead of working together, they each try to complete their objective separately. Meanwhile, Jenkins is frustrated that objects keep mysteriously disappearing from the library.
A massive storm rises up out of nowhere. It is obvious that it is magical in origin and linked to their mission somehow. Flynn realizes that the man who put together the exhibit is a fictional, a being that came to life out of a work of fiction. After some misadventure, the man identifies himself as James Moriarty.
But Moriarty is not the one pulling the strings. As the storm worsens, New York is in dire peril. Flynn eventually puts the clues together and determines that the true power behind all of this is Prospero, a magician from Shakespeare's The Tempest. Prospero is using everything that's going on to gain power.
Prospero, who was disguised as the museum's janitor, makes his escape, along with Moriarty. The storm, unfortunately, has reached critical mass and won't dissipate even though its magical source is gone. The Librarians work together and successfully dispel the storm using a sun stored in the Library and the lamp on the Statue of Liberty.
The team realizes that the work best together rather than separately, and they still have to take down Prospero.