"End Game" featured guest appearances by Megan Leitch, Peter Donat, Brian Thompson and saw Steven Williams reprise his role as X.

The show centers on FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) who work on cases linked to the paranormal, called X-Files.

In this episode, Scully is kidnapped by an alien bounty hunter and Mulder offers his sister Samantha (Leitch) forward as ransom.

However, Samantha is merely one of several clones created as part of a human-alien hybrid project, leading Mulder to pursue the bounty hunter for the truth about her disappearance.

USS Allegiance, an American nuclear submarine, is patrolling the Beaufort Sea off the coast of Alaska when it comes across a craft below the ice that is emitting a radio signal.

Continuing from the cliffhanger ending of "Colony", Dana Scully (Gillian Anderson) is beaten and kidnapped by "Mulder", who is really the Alien Bounty Hunter in disguise.

When the real Mulder (David Duchovny) finds the wrecked hotel room, his sister Samantha explains that the Bounty Hunter will set up a hostage exchange to swap Scully for her.

Finally, Samantha reveals that the clones are the progeny of two original aliens and worked at abortion clinics to gain access to fetal tissue.

Mulder, realizing he has been duped, initially refuses to help and starts to leave, but is knocked unconscious by the arriving Bounty Hunter, who proceeds to kill the Samantha clones and burn down the clinic.

He is discovered and rushed to the field hospital seen at the beginning of "Colony", where Scully—having learned that the alien blood contains a retrovirus that dies in cold temperatures—convinces the doctors to take him out of the bath that would warm his body up.

[3] The stiletto weapon, often referred to as the "gimlet", used by the bounty hunter was constructed from aluminium and acrylic, and activated by a pneumatic hose hidden in actor Brian Thompson's sleeve.

[6] The grunt Scully utters when thrown through a table was insisted on by Standards and Practices, giving the reasoning that the show needed to make it clear for the viewers that she was not dead.

According to executive producer Frank Spotnitz it was an "arcane, bizarre logic that you have to deal with when you're putting a show on network television.

[7] Williams' background in fight choreography, stemming from his role in Missing in Action 2: The Beginning, allowed him to help in choreographing the brawl.

[8] One hundred and forty tons of snow and ice were trucked into a soundstage to create the scene with the submarine towards the end of the episode,[6] and the stage had to be refrigerated for five days.

In a retrospective of the second season in Entertainment Weekly, the episode was rated an A−, being called "an exhausting, essential chapter, boasting the series' most visually stunning finale".

[11] Michelle Bush, in her book Myth-X, has noted that "End Game" is "a good example of the basic premises that Mulder and Scully cannot succeed without the other", and serves to highlight "the danger of making someone else's choice for them.