While Arthur and Mulder talk, on the TV in fron of them plays the scene from the X-Files season 2 episode Colony when the Alien Bounty Hunter shapeshifts from the FBI Agent he had just killed back into himself and locks the car trunk with the agent's dead body inside.
The name of the CIA agent in this episode-Ambrose Chapel-is a reference to the earlier film. In both cases, the name used is a false one. In the film, it is revealed to be the name of a church and not a person. In this episode, it is used as an alias by the Alien Bounty Hunter in disguise.