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Directed by Kim Manners
Doggett: They got it controlled. Nobody goes in or out of that building without them knowing about it.
Scully: HOW DO YOU KNOW THAT THEY'RE YOUR MEN?
The search for Mulder is complicated by the involvement of a shape-shifting alien bounty hunter.
- Agent Scully: Interestingly, the trope namer is not fulfilling this role here. The role is played by Agent Doggett.
- Anti-Hero: Doggett is a good man just following orders from a Bad Boss and comes to know how he is also being used in this game by Kersh and other higher authorities. He ends up getting assigned to the X-Files along with Scully. Despite his rigid and uptight personality he genuinely wants to find Mulder and the truth, help Scully.
- Bittersweet Ending: On the bitter side, Skinner and Scully are brutally beaten by the Alien Bounty Hunter and the search in Arizona is called off, leaving Mulder tragically lost to Scully aboard the alien vessel. On the sweet side, Scully has killed the, or at least an Alien Bounty Hunter and saved Gibson Praise from the aliens. Special Agent Doggett is also assigned to the X-Files, vowing to help her find Mulder.
- Continuity Snarl and Dropped a Bridge on Him: This episode ignores the previous established rule from Mr X that a gun, even shot at the back of the neck, will not kill the Alien Bounty Hunter. He is dropped unceremoniously in a single shot from Scully.
- Killed Off for Real: The Alien Bounty Hunter is finally killed off in this episode by Scully. Whether it is the original Alien Bounty Hunter is left unknown, as the ending reveals several figures of him with the same form on the UFO, observing Mulder.
- Plot Armor: Scully isn't blinded and burned by the Alien Bounty Hunter's blood the way everyone else is.
- Put on a Bus: The Alien Bounty Hunters are never seen again after this episode.
- The Promise: Doggett makes one to Scully that he will find Mulder.
- Myth Arc: Mulder's disappearance due to extraterrestrials taking him away drives the episode's story.
- Say My Name: Scully yelling Mulder's name in the desert where she thinks he may be returned, and Mulder on the ship yelling her name as well.
- Wham Shot: All the aliens at the end gathering around a helpless Mulder have the same default shape shifting appearance as the Alien Bounty Hunter, throwing into doubt whether it was the same one all along since his first appearance.