Caffrey and Cavennaugh follow a lead on an infectee to an Indiana town with a preacher relating visions of an alien landscape.
- This episode opens with Caffrey awakening disoriented and handcuffed in a church basement in New Harmony, Indiana. Injured and alone, she yells out for help.
Two days earlier, a Threshold agent goes missing in New Harmony, Indiana while he was surveilling the mother of Craig Sonntag, one of the infected, missing crew members of the U.S.S. Big Horn. Concerned about her mental health after she had to order the shoot-down of a private jet carrying her good friend, Baylock (Charles S. Dutton) tells Caffrey (Carla Gugino) to join Cavennaugh (Brian Van Holt) in investigating Sonntag's hometown. There, they encounter Rev. Lavory (James Frain), who is captivating his parishioners with his visions of a "sea of glass" and an impending apocalypse. Posing as a reporter, Caffrey gets a closer look at the preacher's meditation garden, where she discovers mutated flies and lettuce sporting bloody, human teeth. After field agent Harper (Murray Russell) oversees a team to turn the church inside out, he sends the team home and lures Caffrey back to the church and knocks her out cold. Meanwhile, Cavennaugh begins to suspect Harper's complicity in the whole thing when Annie Sonntag, the crewman's mother (Deborah Strang), turned out to be infected even though the hair sample, which Harper supposedly collected from her, had turned out to be negative for alien mutation.
Cut back to the opening scene, where Caffrey is being held against her will. She looks over and sees that the missing agent has mutated and is dead. While attempting to free herself, she comes face-to-face with Crewman Sonntag (Kevin Durand), who is about to inject her with his infected blood so that he can learn everything about Threshold. Caffrey is able to fend him off long enough for Cavennaugh to arrive and kill Sonntag.
Meanwhile, when it's suspected that crystals formed on washed-up wreckage of the Big Horn are capable of spreading infection, Fenway (Brent Spiner), Pegg (Rob Benedict) and Ramsey (Peter Dinklage) search the ocean floor to find the remaining pieces of the ship. When they finally discover the wreckage, they are shocked to find crystalline structures growing on the ship at an alarming rate. They decide that it would be too risky to salvage the wreckage and that it would be better to set up an unmanned monitoring station instead.
With these two events, the team believes that the aliens intend to bioform and terraform at the same time.