S4E1 · Herrenvolk

In rural Alberta, Canada, a telephone lineman is stung by a bee as he works at the top of a pole. Five identical boys approach and watch as the lineman adversely reacts to the sting, causing him to fall to the ground and die. The boys look down at his body, then walk off silently.

At a remote industrial site, Fox Mulder (David Duchovny), Dana Scully (Gillian Anderson) and Jeremiah Smith (Roy Thinnes) are approached by the Alien Bounty Hunter (Brian Thompson). Mulder and Smith flee with both Scully and the Bounty Hunter in pursuit, eventually reaching a waterfront. Mulder sneaks up on the Bounty Hunter and stabs him in the neck with the alien stiletto. Both he and Jeremiah escape on a boat, leaving Scully alone with the seemingly dead Bounty Hunter. When she approaches the body, the Bounty Hunter wakes up and chokes her, demanding to know where Mulder and Smith are heading. He releases her after realizing she has no such knowledge.

On the boat, Mulder and Smith debate whether they should save Mulder's mother Teena, despite the risk of Men in Black awaiting them. Mulder ultimately agrees that it would be too dangerous to visit her. Instead, they head towards Canada in a stolen car, where Smith says Mulder will find his sister, Samantha. Meanwhile, the First Elder (Don S. Williams) meets with The Smoking Man (William B. Davis) in Teena's hospital room, confronting him with photos of his prior meeting with her, taken by X (Steven Williams). They realize that there is a leak, and plan to smoke out its source by releasing false information about Teena being in danger.

The Bounty Hunter learns of Mulder's whereabouts by listening in on a phone call between him and a captive Scully, leaving her to pursue him and Smith while Scully informs Mulder that the Bounty Hunter is still after them. In Washington, Scully reports to Walter Skinner (Mitch Pileggi), who informs her that the other Jeremiah Smiths have all disappeared. Scully and Agent Pendrell investigate the data that the Smiths were compiling, trying to decipher the encrypted files. Scully contacts X, who tells her that it is related to the government's long-running smallpox eradication program. X also tells her that he believes Teena's life is in danger.

Meanwhile, in Canada, Smith and Mulder's car runs out of gas. Walking the last few miles on foot, they come across the body of the electrician, grossly decomposed and covered in ants. Smith takes Mulder to a mysterious field where they find a group of identical children; the girls all resemble Samantha at the age when she was abducted. Smith tells Mulder that the cloned children are drones, workers used to tend the fields, incapable of speaking. After retrieving a gasoline can, Mulder tries to take one of the female clones with him, against Smith's wishes. However, the Bounty Hunter arrives and chases them. As he corners them in a large bee hive, the Bounty Hunter is crushed and stung repeatedly in a trap set up by the trio.

Scully and Pendrell report to Skinner and the Office of Professional Responsibility on the data being tracked by the Smiths, which appears to be a cataloging of human beings. Meanwhile, the Bounty Hunter catches up to Mulder, Smith and the clone, plowing into their car with a van. After knocking Mulder unconscious, the Bounty Hunter pursues a fleeing Smith. Mulder returns to the hospital to see Teena, resigned to the fact that he cannot save her. The Syndicate leads X to a trap at Mulder's apartment, where he is shot by the Grey-Haired Man. X crawls into the apartment and writes the letters "SRSG" in his blood before dying.

The letters lead Mulder to Marita Covarrubias (Laurie Holden), the assistant to the Special Representative of the Secretary General of the United Nations. Covarrubias tells Mulder that the fields in Canada have been abandoned but shows him a picture of the drone children tending to the shrubs. At the hospital, the Smoking Man directs the Bounty Hunter to heal Teena, telling him that the fiercest enemy is the one with nothing to lose.