In a small house in Ellicot, NY, Gary Sacks tends to his ailing father, Arlen. Gary goes into the kitchen, and Arlen panics when he sees something on the ceiling. Gary hears the heart monitor flatline in the other room and sees that his father has disappeared from his wheelchair. Gary looks for him and hears a hissing sound. Suddenly, a huge reptilian face lunges at him, and he is sprayed with venom.

At the FBI, Scully cleans out her desk in preparation for maternity leave. She finds memorabilia from past cases, and gives Doggett an Apollo 11 key chain that was given to her by Mulder (in 4X17). The medallion symbolizes teamwork and partnership, and she thanks Doggett for his help over the past year. She exits the office. Moments later, Agent Leyla Harrison enters, having been assigned to partner with Doggett on the X-files during Scully’s leave. Harrison, a fan of Mulder and Scully’s work, is excited about being on an actual X-file and accompanies Doggett in examining the crime scene at the Sacks’ home. There are some remnants of slime in the home and near where Arlen’s body was found. Based on her study of Mulder and Scully’s past cases, Harrison immediately jumps to otherworldly conclusions about the nature of the slime. Doggett shoots down her theories.

Doggett wanders alone toward a deserted mansion near the crime scene, and after entering, finds a book on the Sixth Extinction on a desk. He hears a noise and pulls out his gun, only to find Agent Harrison. He tells her that “it” is here and orders her to wait outside. Gunshots ring outside, and he looks for Agent Harrison, but she has disappeared. He goes into the nearby woods and accidentally falls through a trap door on the ground. He finds himself in some sort of underground wine cellar.

Mulder assists Scully in going to her Lamaze class. She admits to feeling like she has deserted her work. Mulder assures her that Doggett can take care of himself. Skinner, meanwhile, leads a pack of agents to search for Doggett. Scully is worried, and expresses a desire to go back to work to help the search. She performs an autopsy on Arlen Sacks’ body and discovers that the slime on his body is actually venom that has been excreted by a reptile. Mulder tries to convince her to stop working as he steps in to conduct his own investigation.

In the underground lair, Doggett is wondering what to make of an amber-colored shell of a dog when he sees something quickly move past him. A giant, snake-like creature attacks him and sprays venom in his eyes. With his sight impaired, Doggett shoots blindly at the creature, and it manages to get away. Harrison hears his gunshots and finds Doggett. Her eyes are also affected, but she brings him to the sickly body of Gary Sacks. Mulder arrives at the crime scene where Skinner is redirecting the search farther away. Mulder, no longer an FBI agent, takes off into the woods on his own and comes upon the mansion. He sees something in the brush and picks it up, but is startled by Herman Stites who claims to own the property. Mulder asks him if he has seen a reptile and the man bristles at any accusations. Mulder walks away and misses Doggett, who has climbed up to a grating and is calling out to Stites from below. “I need a hand,” he begs Stites, who ignores the plea. Stites steps on Doggett’s outstretched hand, and the agent falls back down in the cellar. Doggett and Harrison hear Stites seal the trap door closed. They then realize that Gary Sacks’ body is gone.

Scully calls Mulder to tell him that Skinner is angry that he is tampering with a federal investigation. Mulder believes that it may be a man and not a reptile that they are looking for. He found the Apollo medallion and believes that Doggett is probably still nearby and that Stites is somehow involved. Doggett and Harrison blindly walk through the tunnel in the cellar. She fears that she is afflicted with the same thing as Sacks, because she has become completely blind. The creature appears once again and Doggett wildly shoots at it, but it gets away. Harrison finds Sacks’ body. It has deteriorated even more.

Mulder sits in his car near the mansion, waiting. Scully discovers that the venom hardens the body’s skin to form a shell. Then, its organs liquefy. She tells Mulder that Stites had been working on creating a new species of reptile. Mulder takes off after something moving in the woods. He watches as a human-sized reptile climbs up the house and into the window of the mansion. As Mulder bangs on the front door, he does not see the creature morph into Stites. Mulder confronts Stites, and Stites brings him into the underground wine cellar. There, Mulder sees Doggett and Harrison, who senses that Stites is really the creature. Suddenly, Stites disappears and the creature crawls along the ceiling. Without an issued gun, Mulder orders a blinded Doggett to shoot at the monster, but Doggett can’t see what he’s shooting at. Mulder demands that Doggett aim for the sound of his own voice. Although Doggett is hesitant about firing towards Mulder, he shoots and hits the creature. It transforms into Herman Stites, who lies there dead.

At the hospital, a healed Doggett checks in on Harrison. She will not return to the X-files. Mulder hands Doggett the Apollo medallion, but he asks that they give it to Agent Harrison. Mulder and Scully visit with Harrison, who asks them about a past investigation. As they reminisce with the agent, Doggett walks away down the long hallway, heading back to work -- alone.