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.
Pete tries to adjust to a new partner while investigating a string of bizarre deaths in Denver. The last words of the victims leads the agents to an old friend. Meanwhile, Artie and Claudia try to stop a lightning storm in the Warehouse.
Pete and Myka try to locate an artifact responsible for victims losing their minds... literally. Meanwhile, Steve and Claudia go to Boston to find Typhoid Mary's knife, which can transfer illnesses and injuries from one person to another.
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 hugger - the man who cuddled Myka's former partner.
A mystery organization launches an attack on the Warehouse Regents, trapping them in a skyscraper. While Myka and Artie try to get them to safety, Pete and Claudia try to find the artifact responsible.
While the team investigates the case of a woman who can disintegrate anyone who angers her, Pete and his mother deal with their issues after being reunited.
Myka and Pete deal with a plague of zombies in Ithaca, while Claudia deals with a new romance, a prophecy of death, and a rejection from a friend.
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 and Myka race to stop Sykes from using his own cache of artifacts to destroy them and the Warehouse.