Doggett has a new partner... and a deadly reptile problem.
In Ellicott, New York, Arlen Sacks is killed by a strange creature, which then attacks his son Gary by spraying venom in his face.
At FBI headquarters, Scully packs up her belongings. Amongst the many keepsakes is a medallion commemorating the Apollo 11 space flight. Scully hands the medallion to Doggett, explaining that it symbolises teamwork.
A short time later, Special Agent Leyla Harrison approaches Doggett and tells him that she is his new partner. They are to investigate a murder in upstate New York. She has been assigned as Doggett's new partner.
They make their way to the Sacks' house, where they search for clues, finding some slime which is sent to an FBI lab for analysis. Harrison explains that she processed Mulder and Scully's travel expenses, while working in the accounting department and as a result has an intimate knowledge of previous X Files cases.
Doggett follows a wooded trail away from the Sacks' home to a mansion. He makes his way inside where, unbeknownst to him, the strange creature is clinging to a wall, observing. Sensing something is amiss, Doggett pulls out his gun and instructs Harrison to stand by the door while he flushes the creature out.
While standing near the door, she hears a noise directly above her and opens fire. Doggett rushes onto the front lawn, where he falls through a trap door.
FBI agents descend upon the area and begin the search for Doggett, who has meanwhile regained consciousness in catacombs below the mansion.
From an autopsy, Scully discovers that Arlen was blinded by a kind of reptile venom. Back in the catacombs, the creature sprays venom in Doggett's eyes, blinding him. Shortly afterwards, Doggett makes contact with Agent Harrison, also blinded. Nearby is a very sick Gary Sacks. Realizing that Gary needs medical attention, Doggett attempts to scale the catacomb walls.
Mulder, meanwhile, searches the area around the mansion for clues and encounters the owner, Herman Stites, who identifies himself as a biologist. Below, Doggett reaches the drain grate and he calls for help. Hearing, Stites stands on his fingers until he loses his grip.
Mulder tells Scully he found the Apollo medallion near Stites' estate, and is convinced Doggett is somewhere nearby. A lab report indicating that the venom found near the creature's victims is unnatural prompts Scully to do some research on Stites. Later Scully phones Mulder to say that Stites is a crypto-biologist specializing in reptile genetics.
Mulder spots the creature and chases it to the mansion where it climbs up to a second floor landing. Mulder bangs on the front door, demanding that Stites let him inside. The creature makes its way through the house, transforming into Stites, who opens the front door and listens as Mulder warns him about protecting the creature.
Stites leads Mulder to the catacombs, where Harrison and Doggett are still trapped, and locks him in. The creature reappears, and Mulder begs the still-blinded Doggett to open fire. Doggett hesitates,then shoots.The creature falls to the ground and transforms into Herman Stites.
The agents visit Agent Harrison in her hospital room... and present her with the Apollo medallion.
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