Pete and Myka return to Washington to intercept a samurai sword that is to be presented to the president, and they discover a competitor for items that belong to the warehouse.

After receiving word that her father is dying, Myka travels home to see her parents.

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?

A super-powered vigilante is at large in Detroit, and the agents try to track down the person responsible. Meanwhile, things between Leena and Claudia are still tense, and Artie is haunted by the spirit of his dead friend.

Pete Lattimer is hit in the head by an artifact and wakes up to a life where he was never born. Pete must hunt down and persuade the Warehouse team (none of whom recognize him) to go on this life or death mission with him to vanquish a long dead nemesis from the past to get everyone’s lives back.

With the fate of the world in their hands, Pete and Myka's only hope of finding a cure to the Sweating Sickness is a drunken history professor. Meanwhile, Steven and Claudia enter Artie's subconscious in an attempt to bring him out of his coma before he fades away for good.