After preparing a museum in D.C. for presidential visit, 2 Secret Service agents are transferred to an isolated warehouse 13 in South Dakota, where Artie sends them to Iowa to collect a supernatural artifact from a law school student.

Pete and Myka are sent to Chicago to investigate a series of odd bank robberies. During their investigation, they have a run-in with Bonnie Belski, a persistent FBI agent looking for a logical explanation for the happenings. It seems the bank robbers are using a device that creates a sound resonance so severe, it sort of hypnotizes all who hear it and leaves them in a state of euphoria for minutes after. It's up to Myka and Pete to figure out where the robbers will strike next and retrieve whatever bizarre object they are employing. Meanwhile, Artie examines a possible security breach back at the warehouse.

Pete and Myka are sent to investigate a small 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 and he seeks help from Leena who may know more about what is going on.

Artie is kidnapped by a woman who blames him for the death of her brother.

The Warehouse team pursues an artifact collector who is trying to gather together sculptures of the four elements thinking they will enable him to find the secret to obtaining god-like powers.

Pete and Myka hunt for a lethal artifact but it finds Pete first. As Pete prepares to sacrifice himself as did the first Warehouse agent who recovered it, Myka searches for a way to save him, if she can find him.

The theft of the perfect Samurai sword attracts Atrie's attention because he suspects his former partner and current nemesis; McPherson.

Pete's goofing around with Lewis Carroll's mirror creates a mishap in the warehouse with bad consequences for Myka, but there's no time to learn of it as Artie has to send his agents out right away to discover how two small-time crooks are suddenly able to rake in millions at the casinos without raising any eyebrows.

A prison, a new warden, and a charismatic preacher inmate who may have a artifact seems related to a string prisoner suicides accompanied by hallucinations. Pete and Myka search for the artifact as an approaching tropical storm accentuates it's influence but get caught up in the mayhem.

While Artie undergoes a Warehouse style performance review things go from a little haywire to seriously bad at the Warehouse.

The Warehouse team narrowly misses nabbing McPherson then Myka's father falls under the influence of an artifact that resists the purple goo.

Mrs. Frederics explains the reason for MacPherson's break with the Warehouse program. Despite some extreme precautions he managed to get his hands on some artifacts that he plans to auction. But to Artie and the team it all sounds like a smoke screen for a more nefarious plan.