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When Mrs. Frederic learns that things are getting serious between Pete and Kelly, she drops by the Warehouse to give him her brand of friendly advice. Her attention is soon shifted, however, when they get a ping about a trio of students who have dessicated in Egypt. And when Mrs. Frederic starts speaking Demotic - a dead, Egyptian language - they realize that it's not just an artifact involved, but a whole warehouse: Warehouse 2.
When Mrs. Frederic's condition worsens, they learn that each warehouse has a caretaker. When Warehouse 2 came back "online," it searched for its caretaker and, finding none, found Mrs. Frederic. In order to save her life, and Warehouse 13, Pete, Myka and HG have to fly to Egypt and shut the warehouse down. Mr. Valda, one of the Regents, meets them to be their guide, aided with an amulet of an ankh and a rough knowledge of Warehouse 2 mythology. One of the most important phrases thereof is "Mind, Body, Soul," and the team realizes the importance when they enter the first chamber of the warehouse. As the ceiling descends upon them, Pete realizes that the posts in the chamber are a test for the mind. Quickly moving the pieces in a manner similar to a game he played as a child, Pete is able to prop the dropping ceiling up and save their lives. Their next test, "Body," is to traverse a corridor full of spinning blades and shooting flames. HG steps up and shoots a grappling hook to the other end, and they begin zipping their way to the next challenge. Valda, however, recognizing the phrase, "One must die," realizes that the warehouse is demanding a sacrifice, and looses his grasp on the zipline, plunging to his death.
At Warehouse 13, Mrs. Frederic continues to be split between warehouses, a situation that could end her life. Vanessa, the warehouse physician, comes to care for her, and informs Claudia that, if the team can't shut down Warehouse 2 in time, Claudia will have to take Mrs. Frederic's place as caretaker.
Pete, Myka and HG face the "Soul" challenge, where they are each presented with their most cherished love, hypnotizing them into bliss as the ground crumbles underneath them. Myka snaps herself out of the reverie, however, and wakes the others just in time. She destroys the hypnotizing device, and the three are able to cross into the stronghold of the warehouse and shut it down. They do so in the nick of time, for at that moment in South Dakota, Claudia was about to take the mantle of caretaker from Mrs. Frederic. She is saved for now, but Vanessa intimates that the time will come for her to step up. Mrs. Frederic follows up by asking about Claudia's research into the students, and the two realize that someone from inside Warehouse 13 has hired them to find, and awaken, Warehouse 2.
HG has slipped away, and when Pete and Myka find her, they're greeted with a regretful countenance. She asks forgiveness as she shoots them with a stun gun, and leaves them unconscious on the floor of Warehouse 2.