Flynn and Eve use a magic orb to travel back in time to 1611 to get their hands on Prospero's magic staff, in order to stop him in the present and save the future. Unfortunately, things don't exactly go according to plan. Moriarty also travels back in time and attempts to kill Shakespeare before Prospero can appear.
Flynn stops Moriarty, and both Flynn and Eve are surprised when they realize that Prospero isn't just another Fictional like Moriarty: he's actually possessing Shakespeare himself. They manage to pass this information on to the other Librarians in the present.
Even as Flynn, Eve, and Moriarty face Prospero in the past, the other Librarians and Jenkins confront him in the present. Things go wrong in the past, and Moriarty is killed. Eve meets the Lady of the Lake, who gives her Excalibur.
Flynn wields Excalibur and shatters Prospero's staff just as the Librarians complete an exorcism spell of Prospero in the present, restoring him to Shakespeare.
The paradox allows Shakespeare to return to the past, but Eve and Flynn are trapped in 1611 due to the destruction of their time travel orb. However, with a little help from Shakespeare, they're able to return the "long way around," and are discovered as a statue behind the mysterious locked door in the Library.
They're restored, and the Library gets back to normal, now with Cal reunited with Flynn, and Eve and Flynn enjoying a renewed relationship.