S8E20 · Essence

While preparing for Dana Scully 's (Gillian Anderson) baby shower, her mother Margaret (Sheila Larken) invites a woman named Lizzy Gill to help Scully around her apartment. Unbeknownst to Scully, Gill tampers with her pregnancy medication. Meanwhile, Billy Miles (Zachary Aynsley), satisfied with the research conducted at Zeus Genetics, kills the head scientist, Dr. Lev, and burns the laboratory. All of the evidence at Zeus Genetics is destroyed, including the viable hybrid fetus. Fox Mulder (David Duchovny) informs John Doggett (Robert Patrick) of the fire, and asks to go along to survey the crime scene. Mulder reveals that Lev is connected to Scully's former obstetrician, Dr. Parenti. While searching Parenti's office, the agents find another storage room containing hybrid fetuses. They confront Parenti, who denies everything.

Back at Scully's apartment, Gill leaves for the day. She gets into a car driven by Duffy Haskell, and tells him she thinks Scully trusts her. At the lab, Agent Crane derides Doggett for dealing with Mulder. Mulder and Doggett head back to Parenti's office, during which time Miles appears and decapitates Parenti. As they enter Parenti's office, they confront Miles—Mulder is thrown through a glass barrier while Doggett shoots him several times with no apparent effect. While Mulder and Doggett are distracted, Miles escapes. The two go to Scully's house to regroup. Gill overhears and contacts Haskell, who is at an illegal human cloning facility. At the other end, Haskell is also decapitated by Miles.

As Doggett, Mulder, and Walter Skinner (Mitch Pileggi) survey Haskell's murder scene, Scully catches Gill in the act of tampering with her medication. Later, Gill confesses that she, along with Haskell and others, have been monitoring Scully's pregnancy as part of the alien colonists ' plans. However, she tells the agents that Scully's baby is a perfect human child with no human weaknesses. Mulder, fearing for Scully's safety, prepares to take her away. Doggett and Crane receive a call from Miles claiming to surrender, but this turns out to be a distraction. Miles instead goes after Scully, just as she and Mulder escape. As Miles is about to catch Mulder and Scully, Alex Krycek (Nicholas Lea) runs him over and takes them to Doggett and Skinner, just before Miles gets back up.

Krycek states that Miles is one of a new type of aliens that are trying to wipe out humanity's ability to survive the invasion—including Scully's baby, which Krycek states is a special child that the aliens fear. Mulder tells Doggett to send for help. Monica Reyes (Annabeth Gish) arrives as Miles shows up at the J. Edgar Hoover Building. Scully is able to sneak out of the building with the help of Krycek, Doggett and Reyes. Mulder and Skinner, meanwhile, lead Miles to the roof, where Mulder pushes him off into a waiting garbage truck, which then compacts him. Scully and Reyes pull away. The episode ends with Crane pointing them to safety, then turning around, revealing to the camera that he is a Super Soldier.