Visible crew/equipment: When Scully asks Fox "Do you know what day it is?" the boom mic drops down at the top of the screen. (00:04:50)
Visible crew/equipment: As Fox is being led into the jail, when Scully says, "Mulder" the boom mic is at the top of the screen, while she's walking towards him. (00:20:30)
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller