S8E1 · Within

Dana Scully (Gillian Anderson) has been deeply distraught since Fox Mulder (David Duchovny) was abducted by aliens. One morning, she arrives in her partner's office to find it being searched by FBI agents. Scully subsequently learns that the Bureau's newly promoted deputy director, Alvin Kersh (James Pickens, Jr.), has launched a manhunt in search for Mulder. The investigation is being led by an FBI special agent named John Doggett. Scully and Walter Skinner (Mitch Pileggi) are taken to the task force 's field office to be questioned, despite protests that they would be the most qualified to lead the manhunt themselves. As Skinner is being interrogated, Scully is accosted by an unnamed person who starts asking her about Mulder. When Scully finds out that he is actually Doggett (Robert Patrick), she angrily throws water in his face and leaves.

Back at her apartment, Scully runs a background check of Doggett on her computer, learning about his background as a former NYPD detective. She feels sick and leaves the computer, and later on calls her mom, Margaret (Sheila Larken). When she realizes her phone is tapped, she looks outside the window to see if anyone is out there. She angrily calls Doggett to protest him monitoring her phone conversations, which he seems genuinely surprised about. She notices a mysterious man and runs into the hall to pursue him, but meets her landlord Mr. Coeben, who claims he had seen Mulder.

Meanwhile, Skinner visits the Lone Gunmen, who are monitoring UFO activity in the U.S. in the hopes of tracking down Mulder. Skinner later finds out that someone has used Mulder's FBI pass to gain access to the X-Files, and that the Bureau task force considers him the main suspect. Meanwhile, Doggett has gathered enough evidence to track Mulder's whereabouts before his so-called abduction, discovering that Mulder was dying and had his name engraved in his family's gravestone to mark his death in 2000. Later on, more evidence of high UFO activity in Clifton, Arizona, is found by the Lone Gunmen. Concurrently, Doggett receives information about Gibson Praise (Jeff Gulka) when someone slips his file under his door.

Scully and Skinner leave for Arizona without giving any of their information to Doggett. At the same time, Doggett believes that to find Mulder they must first find the whereabouts of Praise. They locate him at a remote school for the deaf in the town of Flemingtown. By the time Doggett's task force arrives, Gibson has already escaped via a window and is leaving for a desert hill top with another person: Mulder.