Mulder races to rescue Scully, who has been kidnapped by Duane Barry, but is too late to prevent her disappearing, apparently abducted by aliens. Mulder realizes that Krycek is working for the CSM. Skinner officially re-opens the X-Files.
- Banging for Help: Scully tries to gain attention by banging when she's Bound and Gagged in the trunk of Duane Barry's car. The cop who stopped the car got distracted.. and he got also killed, poor guy.
- Berserk Button: Mulder goes a little crazy upon seeing that scrap of Scully's bloodied hair.
- Downer Ending: The only thing saving it from being completely depressing is Mulder getting back the X-Files, but that's of little comfort to him in the final scene.
- Frame-Up: Mulder strangled Duane, who Krycek secretly killed soon afterwards. The intent isn't to leave Mulder looking absolutely guilty but to leave enough doubt that it taints his already damaged reputation.
- "Hell, Yes!" Moment: "As of this minute, I'm reopening the X-Files."
- Heroic BSoD: Mulder after Scully is abducted.
- I Did What I Had to Do: Duane shows some remorse for handing Scully over to the aliens and hopes that she survives whatever they'll do to her. He was just completely unwilling to go through that again himself.
- Jerkass Has a Point: Skinner tries to keep Mulder off the case because he's too emotionally invested in it. Given that Mulder later strangles Duane, Skinner had a point.
- Karma Houdini: Krycek disappears into government-sponsored thin air after his murders and deceptions are in danger of exposure. Lampshaded by an incredulous Mulder.Mulder: Who are these people who can just murder with impunity and we can't do anything about it?
- Laughing Mad: Duane, believing himself finally free of the aliens, has this reaction.
- Reasonable Authority Figure: Recognizing what has happened, Skinner does the only thing he can: reopen the X-Files.
- Special Edition Title: The title sequence ends with "Deny Everything" in the place of the usual "The Truth Is Out There."
- Stock Episode Titles
- Tragic Keepsake: Scully's necklace.
- Unstoppable Rage: Mulder goes absolutely ballistic on Duane after catching sight of evidence that he harmed Scully. Krycek exploits it to disguise his poisoning shortly after.
- Wham Episode: Scully is abducted and Skinner reopens the X-Files.
- Why Don't You Just Shoot Him?: When all is said and done, Krycek prefers to just kill Mulder but is overruled. CSM prefers to avoid "turning one man's religion into a crusade."
- You Are Not Alone: Inverted. X tells Mulder that no one can help him this time.