One Breath - S2-E8
Other mistake: At The Beginning of the episode, a gravestone for Scully is shown. However, it seems as if less than a week passes between Scully's mother and sister deciding to let her go and Scully waking up. It's unlikely that the gravestone business would have the stone ready in such a short time.
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