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 Figit" 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.
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.