In S3E1, Steven Jinks replaces Myka in the warehouse 13. He is ATF agent and he is blessed with the power of recognizing the person lying. Pete and Steve undertakes their new mission in Denver and in this mission Steve has been saved by Myka. Meanwhile Artie, Claudia and Leena are dealing with dreadful statues back in the warehouse 13.

While Pete and Myka go after someone using an artifact to induce Alzheimer's, Claudia goes on her first case as a full agent with Steve to track down Typhoid Mary's knife.

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 Claudia and Steve attempt to infiltrate a Civil War reenactment to recover U.S. Grant's flask, Pete and Myka must deal with Pete's ex-wife... who has been stung by an artifact bee that has turned her into a human queen bee.

Pete, Myka, and H.G Wells rush to ward off the death and destruction of Joshua's Trumpet

Fargo becomes trapped in a video game inspired by Warehouse 13 and requires help from Pete, Claudia and Myka. Meanwhile, Stukowski recruits Artie and Steve to help with a case, and catches them stealing an artifact.

Myka and Pete have one last chance to catch a dangerous killer--the man who murdered Myka's former partner.

In S3E8, Sally Stukowski has been questioned by the agents of the warehouse 13. She has been held liable to kill the regents of their team by using that artifact. But soon the agents find themselves in the trap prepared by her to caught them in the building. In the mean time Steve is not happy with the plan of Mrs. Frederic.

The Warehouse team must determine how anyone who angers a woman is instantly vaporized.

Pete and Myka track a troublesome taco truck while Claudia reaches out to Jinks.

As Sykes begins his end game, the agents discover that Helena is still alive... and teaching high school literature. Meanwhile, Jane reveals the full extent of her plan but one agent will lose their life carrying it out.

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 everyones lives back.