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Directed by Rob Bowman
Mulder: I got to get up there.
The Alien Bounty Hunter abducts Scully and holds her hostage in exchange for Samantha. Mulder learns that the clones from the previous episode were human-alien hybrids, part of an attempt to establish an alien colony on Earth — and that his apparently-returned sister Samantha is another such clone. Following this discovery, he recklessly pursues the Alien Bounty Hunter for answers.
- Abusive Parents: The scene where Mulder confesses to his father that Samantha's gone again makes it pretty clear that the Mulder family was not just dysfunctional but pretty emotionally abusive."Do you realize what losing her again is going to do to your mother? Do you?"
- Alien Blood: Scully spends much of the episode examining the Alien Bounty Hunter's blood and trying to find a cure.
- The Bad Guy Wins: The Alien Bounty Hunter easily accomplishes all the objectives he set out to do for both episodes and escapes to his ship, in spite of the heroes best efforts. X even warns Mulder that fighting the Alien Bounty Hunter was a battle he 'could not win'.
- Big Damn Heroes: When X refuses to help Scully find Mulder, Skinner shows up and fist fights him until X decides to relent.X: I've killed men for far less.
Skinner: You pull that trigger, you'll be killing two men. Now I want to know where Mulder is.
- Bittersweet Ending: On the bitter side Mulder has seemingly lost his sister another time, is brutally beaten by the Alien Bounty Hunter and poisoned with his blood and is left with few if any answers across the two episodes, but on the sweet side Scully saves his life and he has found "faith to keep looking".
- Bullying a Dragon: Mulder is alive by the end of the episode only because of the Alien Bounty Hunter's professionalism and restraint.
- Curb-Stomp Battle: The Alien Bounty Hunter effortlessly overpowers and defeats both Scully at the hotel and Mulder on the submarine, flinging them around like children, once he drops the act of the disguise he is wearing. Even pointing out how many times he could have simply killed Mulder throughout both episodes. To say nothing of wiping out the entire crew of a nuclear submarine that was dispatched to destroy his UFO.
- The Determinator: Mulder, despite how suicidal it is to do so, and having been beaten by the Alien Bounty Hunter before, will not stop chasing him for answers about his sister. Pursuing him all the way to the Arctic, where he is brutally beaten and exposed to alien toxins for his efforts. To the point it seems to impress even the Alien Bounty Hunter, who lets him live.
- Flatline: Mulder, after the doctors ignore Scully's advice to put his body in cold environments instead of warm ones. He gets better after the doctors reconsider.
- Friend-or-Idol Decision: Mulder has to decide to risk his newly-found sister if he wants to save Scully from the Alien Bounty Hunter.
- Jerkass Has a Point: Despite how cold and hostile Mr X is, he is proven absolutely right about Mulder's chances against the Alien Bounty Hunter, and the foolishness of pursuing him.
- Late-Arrival Spoiler: In order to watch this episode on DVD, you have to click on a still from the episode showing Samantha Mulder's face bleeding green blood, revealing not only that the Samantha featured in this and the previous episode was fake, but also that she dies.
- Manly Tears: Mulder sheds these when confessing to his father that he lost Samantha again.
- One-Man Army: Well, one alien army. The episode that really shows what the Alien Bounty Hunter is capable of.
- Prisoner Exchange: Mulder performs such a trade in between Scully and the alien clone of his sister Samantha. It doesn't go too well.
- Punch-Clock Villain: The Alien Bounty Hunter racks up quite a body count in this episode, but he avoids gratuitously killing humans unless they stand in his way. At the climax, he repeatedly tries to talk Mulder out of his search for Samantha, only relenting when it's clear Mulder won't give up no matter what he says or does. Leading to the Alien Bounty Hunter telling him what is ultimately revealed to be a comforting lie, that Samantha is still alive.
- Wham Shot:
- Mulder follows Samantha's only lead: the Women's Health Services Clinic. He walks into a room with a worker having her back turned on him. He asks her to turn around... and she takes off her face mask, revealing it's Samantha.
- Now in disbelief over this sudden reappearance, she proceeds to show him that she didn't mysteriously come back from the dead... by showing him another clone of her. And then another one appears behind that one, all but confirming that the woman Mulder was with in the past episode wasn't real.
Mulder: No. No. But I... I found something I thought I'd lost. Faith to keep looking.