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Mulder: Sounds just like an X-File.
The deaths of several doctors in separate states who are physically identical put Mulder and Scully on the trail of a secret cloning program and an unstoppable shapeshifting alien assassin (Brian Thompson).
- Cliffhanger: Scully finds out that she is now at the mercy of the Alien Bounty Hunter, who is in her room and impersonated Mulder to reach her.
- Cloning Blues: The Gregors are working to clone alien-human hybrids. It's unclear whether the Gregors are themselves clones or if they're merely aliens who take identical forms.
- Continuity Nod: Mulder initially believes Chapel's story about the Gregors being a Soviet cloning experiment because "we've seen things like this before."
- The Dreaded: The Alien Bounty Hunter full stop, from how the clones all react to seeing his default form, or recognizing him in one of his disguises.
- Dysfunctional Family: The Mulders, oh so very much. A father who won't hug his son? In this episode viewers find out that his parents are divorced.
- Flat Line: Mulder flat-lines in the Cold Open.
- How We Got Here: The episode starts with Agent Mulder being brought to the ER, with Scully trying to warn the doctors not to immerse him in warm environments. As they do, he flatlines, and this episode and the next all lead up to this point.
- Manipulative Bastard: The Alien Bounty Hunter is a master at this, getting even Mulder and Scully and a number of others to do a great deal of the work for him locating his targets, thanks to his shapeshifting abilities, experience and cunning.
- Myth Arc: A very thrilling mythology episode introducing the Alien Bounty Hunter, containing green blooded aliens/hybrids, and a woman who claims she's Mulder's sister.
- Oh, Crap!: After receiving a phone call from Mulder, Scully can only turn around in suppressed shock at the man behind her, who looks like Mulder but never called her at this time. This is where she discovers that the Mulder standing there is an impostor.
- Red Herring: Since several of the Gregors work in abortion clinics, Mulder and Scully briefly suspect a fanatical priest who made threats against one of the doctors. Later, Chapel (who's the Alien Bounty Hunter in disguise) tells Mulder that the Gregors were a Soviet cloning experiment from the Cold War and that the Bounty Hunter is a Russian assassin sent to destroy them.
- Shapeshifter Default Form: He looks very menacing. Fans nick-named him Schwarzen-alien as his actor bore an uncanny resemblance to Arnold Schwarzenegger.
- Shapeshifting: The Alien Bounty Hunter makes his first appearance. He took the form of one federal agent whom he killed and used it to trick Agent Mulder. At the end of the episode, he forms himself into Mulder and tries to trick Scully. Had Mulder not been calling her, she wouldn't have recognized him as an impostor. This was one of the show's biggest ParanoiaFuels.
- Shout-Out: Ambrose Chapel's name is a reference to The Man Who Knew Too Much.
- Super Window Jump: One of the clone doctors jumps from the fourth floor unharmed to escape the alien bounty hunter.
- To Be Continued: First of a two-parter which ends up with Scully being attacked by Mulder's look-alike. And we know from the beginning of the episode that Mulder is dying!
- The Un-Hug: Agent Mulder is called by his father to visit his mother due to a family emergency. When he arrives, Mulder greets him and goes for a hug. Bill Mulder, however, just extends his arm. They shake hands, but Mulder is visibly disappointed.
- Wham Line:
- Mulder is called to his family home because of an emergency, where his father, William, greets him. William apologises for calling the situation an emergency, while Mulder can see his mother speaking to a unknown woman from behind. This leads into the following exchange:Mulder: Who is Mom talking to?
William: (Puffs cigarette) Your sister.
- Mulder seemingly arrives at the hotel where Scully is staying. After saying hello to him, Scully receives a phone call, which completely flips the script on who is really where.Mulder (phone): Scully, it's me, where are you?
- Mulder is called to his family home because of an emergency, where his father, William, greets him. William apologises for calling the situation an emergency, while Mulder can see his mother speaking to a unknown woman from behind. This leads into the following exchange: