An FBI task force is organized to hunt for Mulder but Scully suspects the task force leader, Special Agent John Doggett, and instead chooses to search for her lost partner with Skinner.
After Fox Mulder's alien abduction at the end of season seven, newly-promoted Deputy Director Alvin Kersh assigns pragmatic Special Agent John Doggett to head up the taskforce searching for Mulder. At the start of the episode, Mulder's desk is being cleared to find evidence which could help the manhunt. Kersh sends Walter Skinner and Dana Scully down to the taskforce office to be interrogated. While Skinner walks down to the interrogation room with Gene Crane, Scully waits. An unnamed person next to her then starts asking her questions about Mulder. When she finds out that person is Doggett, she throws water in his face.
Back at Scully's apartment, she uses her computer to run a background check on Doggett. She then feels sick and leaves the computer and later on calls her mom, Margaret Scully. When she founds out her phone is tapped, she looks outside the window to see if anyone was out there. She sees a mysterious man, and she runs down the hall where she meets her landlord Mr. Coeben who tells her that it was Mulder he saw in the hallway.
Meanwhile, Skinner visits The Lone Gunmen, who are checking for any UFO activity in the United States which could be connected to Mulder's abduction. Skinner later finds out that someone has used Mulder's FBI pass to get into the FBI to reach some X-Files, and Skinner has become the main suspect. Doggett on the other hand gathered enough evidence to track Mulder's whereabouts before his abduction. He finds out that Mulder is dying
and that he engraved his name in his family's gravestone to mark his death in 2000. Later on, The Lone Gunmen state they are seeing increased UFO activity in Arizona. In the meantime Doggett gets information about Gibson Praise when someone slips Gibson's file under his door.
Scully and Skinner leave for Arizona without giving any of their information to Doggett. Doggett believes that to find Mulder they must first find the whereabouts of Praise. The eventually locate him in Flemingtown, Arizona in the middle of the desert. By the time Doggett's taskforce has arrived, he had already escaped via a window and left for a desert hill top with another person.
Doggett, alone, follows tracks to the desert hill, finding Mulder with Gibson Praise. He draws his gun and demands that Mulder let the boy go as the episode closes.
This episode marks the first major change to the opening credits since the show first started with new images, updated photos for David Duchovny and Gillian Anderson and the addition of Robert Patrick to the main cast. After David Duchovny's departure as a main character after the seventh season, Carter and most fans felt the show was at its natural endpoint, but it was decided Mulder would be abducted at the end of the seventh season, leaving things open for the actor's return in 11 episodes the following year. (Fox Mulder 'Ready to Get Back to Work') They eventually replaced Duchovny's Mulder with Robert Patrick's John Doggett. (Patrick marks 'X-Files' spot) Jim Engh was a member of the production crew of The X-Files and died during filming of the episode. He was electrocuted to death, six other crew members but no other deaths. This episode was dedicated to his memory. (The Truth Behind Season 8)
Chris Carter was inspired to write the scene in which Dana Scully splashes water into Doggett's face, due to Carter being aware that new actor Robert Patrick would be facing opposition from some members of the fan community. After the conclusion of The X-Files television series in 2002, Patrick commented that this part of the episode had been his favorite scene he had ever shot for the series, admitting that he couldn't think of a better way to introduce the character and that the scene not only said a lot but that it had actually helped him, and Tom Braidwood, who appears in this episode as long-running recurring character Frohike, similarly remarked that the first meeting of Doggett and Scully was one of his own favorite scenes from the entire series.(The Complete X-Files: Behind the Series, the Myths and the Movies, The Truth Behind Season 8)
- When last seen in the episode The Beginning, Gibson Praise was in the custody of the Syndicate and using his telepathic abilities to monitor the EBE at the Rolling Hills Nuclear Power Plant. While the briefing that Agent Doggett gets details Gibson's previous whereabouts, there is no explanation given as to how he came to be living at the school for the deaf in Arizona.
- David Duchovny as Special Agent Fox Mulder
- Gillian Anderson as Special Agent Dana Scully
- Robert Patrick as Special Agent John Doggett
- James Pickens, Jr. as Deputy Director Alvin Kersh
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Bruce Harwood as John Fitzgerald Byers
- Kirk B.R. Woller as Agent Gene Crane
- Jeff Gulka as Gibson Praise
- Jonathan Palmer as Principal
- Marc Gomes as Agent Danny Mosley
- Christine Firkins as Thea Sprecher