Douglas Fargo of Eureka's Global Dynamics is sent to Warehouse 13 to help update its aging computer system. This triggers a seemingly sentient computer virus that sends the Warehouse into lockdown and traps the team inside.

While Artie and Claudia meet with Vanessa Calder and Hugo Miller to investigate a computer virus that transforms people into clay, Myka and Pete wake up naked in bed and try to find a missing Steve.

While Pete and Claudia help Hugo Miller track down a bag of marbles at a boy's academy, Myka and Steve travel to New Orleans on the trail of another artifact while Artie meets with Brother Adrian.

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.