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Directed by R. W. Goodwin
Mulder: The larger plan? You mean colonization.
Jeremiah: Hegemony, Mister Mulder. A new origin of species.
Pursued by the unstoppable Alien Bounty Hunter, Jeremiah Smith takes Mulder to see a secret Syndicate project with a population of child clones.
- The Bad Guy Wins: Mostly. The Alien Bounty Hunter/Colonists and the Syndicate come out of this episode much further ahead than Mulder.
- Bee Afraid: The climax takes place in a bee hive.
- Bittersweet Ending: On the bitter side the Alien Bounty Hunter finds and easily defeats Mulder, before presumably killing all the clones, while the Syndicate covers up the existence of the farms and experiments with bees, Mr X is outed as a traitor to the Syndicate and gunned down at Mulder's apartment building. On the sweet side it is eventually revealed Jeremiah Smith escaped the Alien Bounty Hunter, Mr X leaves behind one final clue leading Mulder to his new informant Marita Covarrubias, who uncovers evidence of the farm's existence, and the Alien Bounty Hunter heals Mulder's dying mother at CSM's request.
- Cloning Blues: More Syndicate alien human hybrid clones turn up for their bee experiments, child ones this time, including more clones of Mulder's sister Samantha. The Alien Bounty Hunter proceeds to do what he does best and kill them all upon finding them.
- Couldn't Find a Pen: X, writing in blood in Mulder's hallway.
- Creepy Child: The army of small identical children, dark-haired girls and blond boys. They have no language and just keep staring blankly at people. They were created to work as drones in a secret government project with genetically changed corn and bees. To creep and psyche Agent Mulder out even more, the girl drones look exactly like his little sister Samantha who was abducted as a child. The situation implies that her DNA was used in said project.
- Foreign Language Title: German for "master race".
- Heroic Willpower: Despite dying from two shots to the gut, Mr X managed to crawl all the way down to Mulder's apartment and sign in his own blood one final clue to Mulder.
- Implacable Man: The Alien Bounty Hunter, as ever.
- The Juggernaut: The Alien Bounty Hunter is particularly unstoppable here, not even dropping a giant bee hive on him stops him from defeating Mulder.
- Killed Off for Real: X, due to two gunshots from the Syndicate Assassin.
- Myth Arc: Key items include X's death, the foreshadowing of how the bees will factor into the Syndicate's plan, and the introduction of Marita Covarrubias as Mulder's new informant.
- Pet the Dog: In the end, the Cigarette Smoking Man asks the Alien Bounty Hunter to heal Teena Mulder, which ends up buying her four more years of life. Also the Alien Bounty Hunter, who is clearly not subordinate to CSM, for going through with it, even if for logical reasons instead of moral ones. And in another one for the Alien Bounty Hunter, after using Scully to find Mulder and Jeremiah's location, he lets her go right away, even though it means she has the chance to tell Mulder that he is on the way.
- Pragmatic Villainy: CSM asks the Alien Bounty Hunter to save Teena, as her death would mean Mulder would no longer have anything to lose and become a greater threat than ever.