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 and Myka race to stop Sykes from using his own cache of artifacts to destroy them and the Warehouse.
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.
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.
While Pete and his mother Jane try to determine the origins of their mysterious opponents, Myka and Claudia travel to Portland to stop a girl who can apparently vaporize anyone she hates with blasts of radiation.
Sally Stukowski and her partner make their move, attacking the Regents and using an artifact to trap them in a building and bring it down around them.
While in Denver, Myka picks up the trail of the counterfeiter who killed her former partner, Sam Martino. Meanwhile, Artie, Claudia, and Steve interrogate a dog that witnessed the theft of an artifact.
Pete, Claudia, and Myka are called in to help Fargo, who is trapped in a virtual reality swords & sorcery game. Meanwhile, Artie and Steve are summoned to New York to recover an artifact... by FBI agent Sally Stukowski.
When a series of mysterious disintegration deaths occur in Pittsburgh, the team discovers that the artifact responsible, Joshua's Horn, has ties to Helena's time as an agent in 1893.
Pete's ex-wife arrives in town to remarry, but an artifact may derail the wedding. Steve and Claudia visit a Civil War reenactment in search of an artifact
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 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.
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.
