Director: R. W. Goodwin
Having located Jeremiah Smith, Mulder and Scully are forced to protect him from an old adversary, the alien bounty hunter. Mulder escapes with Jeremiah Smith, who is their only link to uncovering the truth about an alien colonization plan and Mulder's only hope of saving his mother's life. Meanwhile Assistant Director Skinner's investigation uncovers five identical men named Jeremiah Smith across the country. Scully discovers evidence that these men have been using the Smallpox eradication program to secretly cataloguing the human race. But why?
Jeremiah Smith takes Mulder to a remote farming estate in Canada, where Mulder sees clones of his sister Samantha at the age she was abducted, Jeremiah Smith tells him that they are a colony of worker drones. But before he can reveal the colonization plans the alien bounty hunter arrives and Mulder watches on helpless as Jeremiah Smith is killed. Meanwhile the Cigarette Smoking Man's own investigation identifies X as a traitor. He is gunned down in Mulder's apartment and leaves Mulder one final ambiguous clue, which leads him to a contact in the United Nations, Marita Covarrubias.
She denies all knowledge of the colony Jeremiah Smith showed Mulder as she hands him a folder containing photographs of the colony. The Cigarette Smoking Man has the alien bounty hunter heal Mulder's mother, concerned that Mulder would be far more dangerous to their plans if he had nothing left to loose.
Vanessa Morley, playing Samantha Mulder, got stung by one of the bees during the scene where Samantha, Mulder and Jeremiah Smith enter the bunker. After the shoot Gillian Anderson presented her an award for 'bravery beyond the call of duty' that had been made up by the props department.
Mulder's third source Marita Covarrubias, a Special Representative to the Secretary General, is introduced in this episode after X is killed.
The season's premiere begins with yet another altered tagline: 'Everything Dies', spoken by the Bounty Hunter and then followed up by Marita Covarrubias who informs Mulder that "Not Everything Dies".
Jeremiah Smith: They know where to find us. They'll be waiting for us.
Jeremiah Smith: Your government men. They'll be waiting at thehospital with your mother. Mulder: What can they do? We're working in the light.They, they can't stop us without exposure, without consequence.
Jeremiah Smith: You have to understand something. I must perish.Whatever the consequences to that end, they are incalculable to thepreservation of the larger plan.
Mulder: The larger plan?(Smith stares at him.)You mean colonization.
Jeremiah Smith: Hegemony, Mister Mulder. A new origin of species.
Mulder: I don't understand...
Jeremiah Smith: I can show you.
Mulder: My mother is dying. I need to take you to see her right now.
Jeremiah Smith: And if they are waiting for us? If they're willing tokill me and then face the consequence of their actions and standbefore your ineffectual justice system, I will be dead. I won't beable to save your mother. The work will go on. The plan will continueto be executed. Or you can stop it.
Mulder: How can I stop it?
Jeremiah Smith: I can take you to a place, show you the work inprogress, where you can see...
Mulder: No, look, there's no time!
Jeremiah Smith: Where you can see your sister!
Mulder: Kill me, let them go.
Bounty Hunter: You'd trade your life for his?
Mulder: For my mother's.
Bounty Hunter: Everything dies.
X: You're going in the wrong direction, Agent Scully.
Sculy: All beginning with the letters S-E-P. You know what these are. Confirm or deny.
X: Smallpox eradication program.
X: Don't unlock doors you're not prepared to go through, Agent Scully.
Scully: What's that supposed to mean?
X: Leave it alone. Protect the mother.