Trust No 1

"They're watching."

Written by Chris Carter & Frank Spotnitz
Directed by Tony Wharmby

"This guy seems to know everything. He even reads your e-mail. How can you, or anybody hope to ensure for Mulder a safe passage home?"

— John Doggett

Scully is approached by a man (Terry O'Quinn) who claims to have information about the super soldiers that he will only reveal to Mulder.

Tropes:

Big Damn Heroes: Doggett swoops in just in time to gun down the Shadow Man before he can kill Scully and Reyes.
Idiot Ball: Scully trusting the Shadow Man over Doggett, allowing her desire to see Mulder again overwhelm her rationality.
Myth Arc: This focuses on the super soldiers and their attempt to flush out Mulder and they almost succeed.
Tonight, Someone Dies: The intro teases that somebody in the episode dies, with Scully reacting with grief. Due to the nature of the intro and episode it is implied to be Mulder, but of course it turns out to be a brand new character made for the episode alone.
Weaksauce Weakness: Apparently, the super soldiers are extremely vulnerable to the iron compound in the quarry rocks.
What the Hell, Hero?: Doggett finally calls Scully out verbally on her refusal to trust him after all the time they've known each other.

"WHAT DOES THIS HAVE TO DO WITH MY SON? WHAT'S WRONG WITH MY SON?! ANSWER ME!"