I just watched this again and it was quite good. I was late getting into the X-Files and I'm not sure if I saw all of the first series.
The best thing about this was that Scully is still unsure of Mulder, still questions him and thinks that he might be a crackpot. Also when they are called in by members of a secret government department, they are still sinister and unknown. Mulder says they may be CIA or NSA or something the government will later deny and cover up. We don't yet know about any conspiracies which everything later became tied into.
Lauren Kyte seems to be under the protection of a ghostly force. Mulder and Scully investigate and learn that her employer, Howard Graves, who was like a father to her, supposedly committed suicide. In actuality, the man was murdered by his business partner and is reaching out from beyond to make sure that justice is done.
Mulder: Do you believe in the afterlife?
Scully: I'd settle for a life here!