A car chases a white light as it moves through the sky in Helena, Montana. The driver, Richie Szalay (last seen in 7X22), snaps photographs of the light until it comes to a halt. It is a UFO, hovering above the trees. Richie gets out of the car and is speechless. The craft gets away before he can take its picture, and Richie yells "This is not happening!" in frustration to himself. He notices a man walking toward the spot where the spaceship landed and Richie calls out to him. As the man runs away, Richie follows, but he stumbles over a woman's body lying naked on the ground.

Back at the FBI, Doggett opens up a desk drawer to find Mulder's nameplate inside. He is somewhat troubled, but is startled by Scully rushing in the office. He won't tell her why he called her, but instead takes her up to Skinner. Both men are reluctant to tell Scully whatever news they are hiding. Skinner finally reveals that there was a UFO encounter in Montana and the man who reported it is Richie Szalay, whom Mulder and Scully met the previous spring in Oregon. "Are you trying to tell me this has something to do with Mulder?" she asks. Richie found Teresa Hoese, the woman abducted the same time as Mulder. She was returned, but she is barely alive.

The agents travel to Montana to see Teresa. Her doctor describes her condition as if someone was performing torturous experiments. She has scars on her cheeks, and there is damage to her soft palette and abdomen, but there are no foreign implants in her body. Scully, Doggett and Skinner pay a visit to Richie, who had been trying to find his friend Gary. Gary was also abducted right before Mulder. Richie had followed UFO sightings to Montana where he came across the craft. Doggett shows Richie plaster castings of footprints from the scene. The prints are of Nike sneakers, and Doggett doubts that the man Richie saw was actually an alien. After the questioning, Scully confronts Doggett about his refusal to accept any explanations outside of the ordinary. Doggett says that she is the one who is afraid to confront the truth about what might have happened to Mulder.

Mulder lies bound in the alien chair, but no experiments are being done. His body has decayed so much that he appears to be dead. Suddenly Scully awakes from her sleep and realizes that it was merely a nightmare. She knocks on Skinner's motel room door, teary-eyed. "What if he's dead?" she cries. Skinner tries to comfort her, assuring her that they still might find Mulder alive. Meanwhile, Jeremiah Smith, the alien healer last seen in 4X01, walks into the hospital wearing Nike sneakers. When a nurse approaches him, he immediately morphs into Teresa Hoese's doctor and tells the nurse that he wants Teresa transferred.

The phone wakes Scully in her motel room. She is notified about Teresa Hoese being moved. Scully meets Doggett and Skinner in the field where Teresa was found. Doggett asks that they listen to another point of view, and introduces them to Special Agent Monica Reyes, who is standing alone on a cliff, smoking. Doggett thinks Reyes has some expertise that might come in handy. Reyes explains that she has been briefed of the case and describes it as "interesting." She characterizes Teresa's injuries as similar to what has been found in cult abuse cases, wondering if perhaps there was some kind of abduction group of followers that Mulder got caught up with. Much to the consternation of Scully and Skinner, Doggett insists that they go after the cult leader. Based on a hunch, Reyes believes that Teresa was meant to be left alive. Scully walks away, telling Doggett that Reyes makes no sense, but Doggett insists that he will not go on a wild goose chase after another Alien Bounty Hunter. Meanwhile, a man named Absalom walks into a small boarding house where Jeremiah Smith is treating the ailing Teresa Hoese. Absalom watches as the alien healer places his hand over Teresa's face. Her bruising magically disappears.

In the hospital, Scully catches Reyes examining Teresa's brain scans. Reyes admits that she is looking for alien implants. Scully questions why a disbeliever like her would be looking for such a thing. Reyes disputes the claim. "Let's just say I don't not believe," Reyes says. "I try to stay open." Reyes explains that she has certain spiritual notions, and although she doesn't have any feelings about Mulder she does sense Scully's fear. She advises Scully to try and stay open too. Later, Reyes drives along a Montana highway. Her car putters off and then immediately turns back on. She sees a bright light in the sky above her. "No freakin' way," she mutters and sets off after it. The light disappears over the mountain, and she sees Jeremiah Smith (wearing Nike sneakers) and Absalom pick up a body stranded in the field. Reyes pulls out her gun and orders them to halt. They manage to escape in a pickup truck, but Reyes sees another body lying on the ground. It is Gary Cory, Richie's friend who was abducted in 7X22.

Scully performs the autopsy on Gary, finding radial scarring on his ankles, wrist and face. This matches what she dreamed Mulder had been exposed to. Skinner and Doggett look on, but she becomes emotional and stops the autopsy. Richie is brought into the medical bay and is stunned by the sight of his friend's body. Scully breaks down. Waiting outside, Doggett is approached by Reyes. She senses that he is hurting for his partner. Reyes compares this to a past case where they unsuccessfully looked for Doggett's missing son. She believes that this is why Doggett is so determined to find Mulder. Reyes shows him a police wanted poster of Absalom, the man she saw in the field. He was the leader of a doomsday cult and the license plate on the pickup truck they were driving is registered to a nearby farm.

At the farm, Jeremiah Smith orders Absalom to move the legion of followers out. "They're coming," he says. "You can't let them find him." Federal agents swarm the farm and round up the people. Skinner, Scully, Doggett and Reyes are among the SWAT team. They find Teresa Hoese, fully healed, in one of the beds. While interrogated by Doggett, Absalom says that he can't explain why it happens. The spaceship drops off the injured abductees, and he comes to retrieve them with the sole purpose of helping them. Doggett doubts his intentions. Although there are cameras on the compound, there is no footage of Teresa being healed. Scully shows Absalom a photo of Mulder and asks if there is videotape of him. Absalom has no answer.

That night, Scully returns to the motel, but the lights in her room do not work. She is amazed to see Mulder standing by the window of her room. Reyes approaches and the image of Mulder disappears. Reyes brings her to see tapes from the compound. Scully recognizes the other man on the tapes as Jeremiah Smith, the Alien Healer. On the videotape recorded during the FBI raid, Smith morphs into Agent Doggett. The agents return to the farm compound to look for Jeremiah Smith. Scully pulls out one unrecognizable man who is wearing the Nike sneakers and he morphs into Jeremiah Smith. He tells her that by exposing him she is putting abductees in danger. "Where's Mulder?" she pleads with the healer, but before he can answer, Skinner asks her to come outside. "You must protect me," Smith says to her. Skinner tells Scully that they found Mulder and she takes off for the field. Mulder is lying on the ground, dead. She runs back to get Jeremiah Smith for his healing powers, but the lights of a spacecraft shine overhead. The ship hovers over the compound and the other agents watch as the light radiates the building. Scully rushes into the room where she had just interrogated Smith. He is gone. Scully cries out in frustration and horror: "This is not happening!"

TO BE CONTINUED