After saving the life of the President, two secret service agents - Myka Bering and Pete Lattimer - find themselves assigned to the top secret Warehouse 13. The Warehouse is a massive, top secret facility that houses dangerous and fantastical objects. Together, Pete and Myka along with fellow agents Claudia, Steve Jinks and Warehouse caretaker Artie, must recover artifacts from around the globe before they can cause catastrophic damage.
When Paracelsus takes control of Warehouse 13, it proves to only be the first step in his plan to recreate the entire world in his image. To stop him, Pete and Myka must follow him back through time to 1541 and prevent him from killing the Regents and becoming the permanent master of the Warehouses.
While Pete and Myka team up with two former Secret Service co-workers to investigate a series of bizarre deaths in Washington DC, Artie agrees to show Claudia how and why her sister had to disappear.
While Pete and Steven check out a life-threatening incident at a renaissance faire, Myka agrees to help Claudia revive her comatose sister. However, they discover that doing so has unexpected consequences that threaten the warehouse and everyone in it.
Pete's former girlfriend Kelly Hernandez asks him to help her find her missing grandmother, and the trail leads into a cancelled telenovela. Meanwhile, Artie forces Claudia to go with Steve to investigate the case of a college student of whose spine broke in the middle of a classroom presentation.
The alternate-timeline Valda makes his move, using Claire as his mindless slave. As Valda sets out to move Warehouse 13 to a new location that he can control, the team races desperately to stop him before it's too late.
While the team deals with the news that Warehouse 13 is moving, Mrs. Frederic has them load their greatest memories of their missions into an artifact for future generations.