Scully dreams that Mulder is trapped in an unpleasant alien vessel, and annoyed to find Mulder's office being broken down to help in a search for him. Kersh, now a deputy director, has appointed a special agent named John Doggett to head the search but threatens to fire Scully and Skinner if anything gets out about alien abductions. Scully's first encounter with Doggett is unpleasant, as he suggests that Mulder never truly trusted her and she suspects him of tapping her phone. Scully's landlord tells her Mulder was in the building, and both Mulder and Scully's computers go missing.
The Lone Gunmen have been tracking UFO appearances in the Pacific Northwest, and Skinner thinks they can use the data to find the ship that took Mulder. Doggett confronts Scully with the question of whether aliens took Mulder, and she retorts that she's seen plenty of unexplainable things during her work on the X-Files. Some files at the FBI go missing after someone using Mulder's pass card accesses the building. Doggett also finds that Mulder's credit card was used to take a trip to where his mother is buried and buy a family tombstone that includes his year of death as 2000.
Doggett digs up Mulder's medical records, and Scully sees that they show that he was apparently dying of his brain condition. Doggett thinks that Mulder might be trying one last dying push to prove his theories or cover them up, but Skinner stands by his UFO sighting. The Lone Gunmen have determined that Mulder's ship is in Arizona, and Scully posits that proof of alien existence is being taken before it becomes proof, and that the aliens are in Arizona seeking out the only good hard proof of alien existence there is: Gibson Praise. Someone slips Praise's file to Doggett, and he sends his task force searching for them as well.
The vicious tests on Mulder continue. Skinner and Scully travel to Arizona to find Praise, as do Doggett and the task force. They both discover that he's at a school for the deaf. Doggett arrives just before Skinner and Scully, and Praise escapes through the principal's office window. Praise is taken by someone and led off into the desert, against his will. Doggett pursues and tells the man to let him go. Turns out it's Mulder. To be continued...
First appearance of Robert Patrick as Special Agent John Doggett; Patrick is best-known for playing the T-1000 in Terminator 2: Judgment Day as well as Colonel Tom Ryan on The Unit. The episode is dedicated to the memory of Jim Engh, a production crew member electrocuted while working on the episode.
Scully had a tombstone, too.
Cumulative Body Count (162/202 episodes, 1/2 movies)
Humans: 1,727Creatures: 114
Grand Total: 1,903