Pete and Myka are sent to investigate a town where the inhabitants' minds are being altered making them act as they please. Meanwhile, Artie is confused by the energy flows going on in the warehouse.

The theft of a sculpture leads Myka and Pete to a sacred Indian cave holding an ancient secret of creation... and destruction.

The team discovers that MacPherson is auctioning artifacts he has siphoned from the Warehouse shelves.

In the season two premiere, we pick up right where we left off. MacPherson has blown Artie to smithereens, and disappeared. Is Leena really a traitor? Where has Claudia gone? How will Pete, Myka and the Warehouse fare without Artie? What other havoc did MacPherson wreak when he was alone in the Warehouse? And is there yet a new villain on the horizon?

The team tries to track down their rogue member, and discover the artifact they have is unexpectedly powerful. Meanwhile, Claudia wonders about her future with the Warehouse team and Pete must choose between Kelly and the mission.

When we last left agents Myka Bering and Pete Lattimer at the conclusion of season 2, Myka had decided to leave the top secret team with little to no warning. As season 3 begins, Artie fills Myka's shoes with 'The New Guy,' which also happens to be the name of the season premiere episode.

In the aftermath of the warehouse's destruction, the Warehouse team races against the clock to find a way to undo time itself and put right what went wrong. However, Artie finds himself facing a difficult decision when he is warned that saving the warehouse will unleash an even greater evil.

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.