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Directed by Kim Manners
Mulder: Because there are no true records. Emily didn't come into this world through any system that keeps them.
Scully: How did she come into this world?
Mulder: Have you asked yourself that?
Mulder investigates the past of Emily, the girl Scully found in the previous episode who is Scully's biological daughter.
- Scully's infertility is brought up again.
- The alien retrovirus from season 2 returns, infecting Detective Kresge and a doctor treating Emily. Because of Mulder's previous exposure to it, he is able to save them.
- One of the Bounty Hunter's disguises is an elderly man with a grey moustache. He had previously assumed this disguise in "Talitha Cumi".
- This is one of the first times that Mulder's newfound beliefs about the truth behind alien abductions make him look like a Flat-Earth Atheist. He will get worse before he gets better.
- This is one of the earliest indications of The Colonists using their own agents instead of using the Syndicate as middlemen. Season 9 would later imply that as early as 1991, the Colonists were starting to get fed up with the Syndicate and were exploring options that would lessen their need for human collaborators.
- Cast as a Mask: The Alien Bounty Hunter does not appear in his Shapeshifter Default Form, as Brian Thompson was either not available or simply not cast to keep the character's involvement a surprise. After he kills Dr. Calderon, he seems content to wear his face for the rest of the episode.
- Character Title
- Dreaming of Things to Come: The opening sequence which shows Scully picking up her cross necklace in sand rather than Emily's cremated remains, foreshadowing the end where Emily's coffin contains only sand.
- Dream Sequence: The opening, with Scully in a sandstorm, finding her cross necklace in the sand, and turning into sand herself and blowing away.
- Erudite Stoner: Frohike is implied to be one.Mulder: Do you know anything about pharmaceuticals?
Frohike: Medicinal or... recreational?
- Friend to All Children: Mulder to Emily, with his impression of Mr Potato Head.
- Hero Insurance: Mulder gets some pretty generous coverage in this one. Normally the No-Holds-Barred Beatdown he gave to Dr. Calderon would have resulted in Skinner reading him the riot act. But since Calderon can't afford any unwanted attention from the authorities, he doesn't report it, so Mulder faces no repercussions.
- Hijacked by Ganon: The two silent, mysterious figures who killed Emily's adoptive parents in the previous episode are revealed to be Alien Bounty Hunters. One of them injects a serum into Emily then quietly slips back into the shadows. The other one becomes the Final Boss.
- Kill and Replace: The Bounty Hunter does this to Dr. Calderon.
- Leeroy Jenkins: Kresge is a bit too triggerhappy when confronting the Bounty Hunter, which ends about as well as you'd expect.
- Meaningful Name: Emily Sim, as in simulation, something artificially created.
- Mercy Kill: Scully tells Mulder that Emily doesn't deserve to live as a test subject or tool for the villains. As a result, Mulder doesn't tell Scully about the medicine he stole.
- Mission Control: The Lone Gunmen briefly serve as this while Mulder is infiltrating the convalescent home that the Colonists are using as a front for their experiments. While Frohike is the only one seen on screen, some subtle arm movement behind him suggests that at least one of the other two is working alongside him off camera.
- Myth Arc: More fallout from Scully's abduction, Bounty Hunters and Clones return, and another failed attempt to create an alien/human hybrid.
- Oh, Crap!: Downplayed. Scully and Mulder talk about how, even though she's dead, Emily is still evidence that the villains' scheme exists. Scully then goes to Emily's coffin and opens it, to find nothing but sand.
- Papa Wolf: Mulder delivers the scumbag Dr. Calderon a much deserved beat down over what he is doing to Emily.
- "Shaggy Dog" Story: Mulder threatens Dr. Calderon and tails him to a secret laboratory so he can steal medicine for Emily. He makes it out with the medicine, but ultimately decides to let Emily die.
- Teeth-Clenched Teamwork: Mulder and Kresge.
- Wouldn't Hurt a Child: Played With. Mulder deduces that the bad guys who killed Emily's adoptive parents need Emily alive for their experiments.
- You Have Outlived Your Usefulness: Dr. Calderon finds himself on the receiving end of this after he inadvertently leads Mulder to the Colonists' secret lab.