While Jenkins discovers there's something wrong with the Library since it returned from the Void, the Librarians all find themselves drawn back together after having been off on their own for months, to solve the mystery of a massive storm that has parked itself over Manhattan.
Prospero summons up other Fictionals in order to retrieve the parts of his Staff from a museum. The Librarians soon find themselves pitted against Frankenstein's monster and Sherlock Holmes' brilliant nemesis Moriarty. Meanwhile Flynn (Noah Wyle) and Baird have a disagreement over how to proceed against Prospero.
Stone, Cassandra and Ezekiel have a proper team-up for the first time in months when they investigate a cave-in at an oilrig site, which has unleashed Hokolonote, a shape-shifting god who grows in strength any time a lie is told. Now the Librarians have to come clean to each other, airing their issues and solving the riddle of the ancient prison that held Hokolonote.
Students start disappearing at Wexler College, an institution started by a mad historian/architect who believed in alternate dimensions. When the Librarians arrive, they discover a young student from the physics department is investigating the bizarre occurrences on her own. Meanwhile, Cassandra gets an offer that's difficult to turn down.
While chasing one of the Library's missing artifacts, Flynn is kidnapped by a mysterious stranger with both amnesia and a collection of all the Library's missing artifacts. Soon all of them are in pursuit of the Staff of Zarathustra before it falls into the hands of Prospero.
An old friend of Baird's is running for Mayor of a small New Hampshire town and finds himself embroiled in a scandal in the form of a missing intern and a literal contract with the Devil. Baird soon finds herself in a battle not only for her own soul, but also for the souls of all the Librarians.
When people begin suffering the effects of accidents and sins in which they have not actually been involved, the team tracks the connection to the perpetually young Dorian Gray, whose magic now works on selfies.
The Clipping Book sends the team to a high-tech research facility, where the researchers have been turned into mindless monsters by some bizarre power source in the center's lab. When they disconnect the artifact, however, they find themselves stuck in a time loop.
The team has scattered, all living the ideal versions of their lives. Soon these "strangers" are drawn together to solve a supernatural mystery – the appearance of Ariel, the sprite bound to Prospero's service. Can the Librarians do what no other human has ever been able – turn their backs on their own ultimate happy endings?
The Librarians discover that Prospero's renewed magic is wreaking havoc with the technology of the world. He is recreating an idyllic forest utopia, whether we want one or not. In order to stop him, Flynn and Baird must travel back to 1611, while the rest of the team battles Prospero in the present. Little do they realize that they can only defeat Prospero in each time by finding a way to work together – separated by five centuries.