With Mulder fired and Scully on maternity leave, Doggett is assigned a new partner to carry out work on the X-Files. They quickly get in over their heads when they're trapped underground by a carnivorous reptile monster.
- Ascended Fangirl: Leyla Harrison is basically this. She knows most of the cases Mulder and Scully have been involved with and the episode ends with her pointing out a Plot Hole from the first movie.
- Call-Back: Scully re-gifts the Apollo 11 medallion she got from Mulder in "Tempus Fugit" to Doggett. Doggett loses it and Mulder uses it as a lead, knowing that Agents Doggett and Harrison are near. Leyla Harrison receives the medallion at the end.
- Continuity Nod:
- To the movie when Harrison asks how Mulder and Scully escaped from Antarctica.
- There's also a reference to Queequeg, Scully's dog from seasons three and four, as she finds his tag while cleaning out her desk, and she still has the fused penny and dime from "Dreamland".
- Doomed Hurt Guy: Gary Sacks bought the big one on Doggett's watch.
- Hand Stomp: Stites does this to Doggett when he's trying to pull himself out of the pit.
- Hanging by the Fingers: Doggett while trying to climb out of the pit.
- Impersonating an Officer: Mulder investigates the crime scene, giving his name as Kersh to the suspect he talks to.
- Monster of the Week: A reptile-man. This was the final MOTW that Mulder was featured in until the Season 10 revival (or the 2nd film since it was a not related to the myth arc as well).
- Plot Hole: Lampshaded. How Mulder and Scully got out of Antarctica in The Movie is brought up, and humorously not resolved.
- Reptiles Are Abhorrent: The monster, originally thought to be some kind of reptile, is actually the crypto-biologist who seemed to be protecting the creature and who is able to transform himself at will.
- Tuckerization: Leyla Harrison was a prolific fanfiction writer in the X-Files online fandom. She passed away of cancer in 2001, and the show created the character in honor of her.