S8E19 · Alone

In Ellicott, New York, Arlen Sacks is killed by an unknown creature that sprays venom on its victims, and his son Gary goes missing. In the meantime, at FBI Headquarters, Dana Scully (Gillian Anderson), preparing for maternity leave, packs up her belongings at the X-Files office. She finds a medallion commemorating the Apollo 11 space flight that was given to her for her birthday by Fox Mulder (David Duchovny). Scully gives John Doggett (Robert Patrick) the medallion, explaining that it symbolizes teamwork. After Scully leaves, Special Agent Leyla Harrison (Jolie Jenkins) arrives and tells Doggett that she is his new partner. The two are soon assigned to investigate Sacks's bizarre murder.

At the crime scene, Doggett finds evidence of the venom, which is sent to an FBI lab for analysis. In her previous job Harrison processed Mulder and Scully's travel expenses during their time on the X-Files, and has thus gained an encyclopedic knowledge of their investigations. Following a wooded trail from the crime scene, the agents stumble upon an upscale mansion and make their way inside. A strange creature clinging to the wall secretly observes their every move. Doggett discovers a study full of biology journals and a copy of the anthropologist Richard Leakey 's book The Sixth Extinction.

He pulls out his gun, sensing that something is amiss. Finding Harrison in the hallway, he instructs her to position herself outside the house while he tries to flush the creature. Moments after Doggett instructs Harrison to stand guard he hears gun shots being fired. Rushing outside, he cannot find Harrison anywhere in the yard. He walks farther to the edge and falls through a trap door at the edge of the front lawn.

During an autopsy, Scully correctly deduces that Sacks was blinded by reptile venom. Meanwhile, Doggett and Harrison, having fallen into old bootlegger tunnels below the mansion grounds, encounter the creature and are sprayed with venom, temporarily blinding them. The two find Gary, in dire need of medical attention, nearby. Noting the agents' absence, Mulder searches the area around the mansion for clues and encounters the owner, Herman Stites, who identifies himself as a biologist. Mulder soon leaves the area as Stites notices Doggett about to escape the tunnels, knocking him back in.

Mulder waits in his car in Stites' driveway until dark, telling Scully that he found the Apollo medallion near his estate and is convinced Doggett is somewhere nearby. He spots the creature and chases it to the mansion, where it climbs up to a second floor. Mulder follows the creature into the house and down into the tunnels, where he encounters Doggett and Harrison. With the creature approaching, Mulder tells the still-blinded Doggett to open fire at him on his command. The blinded Doggett then shoots the creature as it leaps at Mulder; the deceased creature then turns into Stites.

Later, Scully and Mulder meet Doggett, who has now fully recovered, at the hospital. He tells them that Harrison will make a full recovery as well but that she is transferring herself off of the X-Files. Mulder attempts to give Doggett the Apollo medallion, but Doggett insists that it be given to Harrison instead. Mulder and Scully then present it to Harrison together, who accepts it in awe.