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The Alien Bounty Hunter

A disguised pursuer who kills clones with deadly alien blood and uses a high-pitched frequency to disable a nuclear submarine.

The Alien Bounty Hunter is a central antagonist in the two-part episode "End Game," which aired on February 17, 1995. Directed by Rob Bowman and written by Frank Spotnitz, this installment features the hunter kidnapping FBI agent Dana Scully while disguised as Fox Mulder's sister, Samantha. The character drives the plot of the series' mythology arc, pursuing clones created for a human-alien hybrid project that dates back to the 1940s. His primary objective is to eliminate these "tainted" progeny and retrieve the specific clone posing as Samantha, leading to a violent confrontation on an American nuclear submarine in the Beaufort Sea.

Species
Alien
Affiliation
Extraterrestrial Race (Sent to cull clones)
First Appearance
Season 2, Episode 17: 'End Game'
Status
Missing/Presumed Destroyed with USS Allegiance
Key Ability
Shape-shifting, High-pitched frequency emission, Toxic alien blood

Lore & Background

According to the narrative revealed by "Samantha," the Bounty Hunter can only be killed by piercing the base of his neck, as his alien blood is lethal to humans. He operates under orders from an extraterrestrial race that considers the cloning experiments on Earth a contamination, necessitating their destruction. The hunter's identity was concealed through a disguise mimicking Mulder's sister to facilitate a hostage exchange for Scully. His presence forces Mulder to realize that the "Samantha" he knew is merely one of several clones working at abortion clinics to access fetal tissue for the hybrid project. The hunter's origins are tied to two original aliens whose progeny were sent to Earth, and his mission reflects an internal alien conflict regarding these failed experiments.

In Their Own Story

The episode continues from the cliffhanger of "Colony," where Scully is beaten and kidnapped by the Bounty Hunter in disguise. After Mulder discovers the wrecked hotel room, he learns from a woman claiming to be Samantha that a hostage exchange will occur on a bridge near Bethesda. During this meeting, the impostor attacks the hunter, but both fall into a river after being shot by a sharpshooter. While Mulder mourns at his father's side, Scully discovers the body dissolving into green liquid. The plot thickens when clones reveal they manipulated Mulder to protect their original; shortly after, the Bounty Hunter arrives, kills them all, and burns down the Maryland clinic. Later, on the USS Allegiance in the Beaufort Sea, Mulder confronts the hunter disguised as a crewman. The struggle exposes Mulder to toxic alien blood. The hunter claims Samantha is alive before submerging the submarine, nearly cutting Mulder in half with its diving plane.

Reader's Guide

To understand this character's role, note that he is distinct from the Syndicate's human collaborators; he is an extraterrestrial enforcer sent specifically to cull the clone population. His defeat requires piercing the base of his neck, a weakness revealed by the fake Samantha before her death. The hunter utilizes advanced technology, including a device emitting a high-pitched frequency that disables nuclear submarines and a pneumatic "gimlet" stiletto weapon. In the final confrontation on the USS Allegiance, he relies on his physical resilience and toxic blood to overwhelm Mulder. His disappearance at the end of the episode leaves no trace of himself or the submarine, though X informs Mulder that a naval fleet was sent to destroy the craft found below the ice.

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