Talitha Cumi

"Nobody's going to die."

Written by David Duchovny (Story) & Chris Carter (Story & teleplay)
Directed by R. W. Goodwin

Jeremiah (as Deep Throat): How many must die at your hand to preserve your stake in the project?
Cigarette Smoking Man: I'm not impressed by your miracles or moved by your trickery. Your justice will be meted out.
Jeremiah (as Deep Throat): By whom this time, and by what tool?
Cigarette Smoking Man: By those who possess the tool of your destruction.

Mulder and Scully investigate a man with mysterious healing powers who is connected to the alien hybrid cloning project.

Tropes:

Combat Pragmatist: X.
Cliffhanger: The episode ends with the Alien Bounty Hunter approaching Mulder, Scully and Jeremiah at knifepoint.
Deadpan Snarker: Mulder takes the CSM at gunpoint and asks whether he'd rather smoke his cigarette or the barrel of his gun. CSM, with mock naiveté, then asks if he's really allowed to choose.
Deal with the Devil: Inverted. It's implied that the devil, dying of lung cancer, accepts a deal from the Ambiguously Human holy man with the power to cure him.
Foreign Language Title: A Syriac or Aramaic expression from the Bible, meaning, "Little maid, arise." In the Bible, it is what Jesus says to a girl he has just miraculously healed.
Foreshadowing: The CSM's conversation with Mulder's mother, which alludes to him having known her in the, er, Biblical sense. The significance of this won't come home to roost until much later.
The Gloves Come Off: We already knew that X was willing to Shoot the Dog, but this episode he turns it on Mulder and starts a vicious fight with him.
Grand Inquisitor Scene: This episode features two lengthy ones, with the Cigarette-Smoking Man and Jeremiah Smith debating the merits of humanity and "the Project" in a prison cell. Closely modeled on the Trope Namer, The Brothers Karamazov.
Cigarette Smoking Man: Anyone who can appease a man's conscience can take his freedom away from him.
Jeremiah Smith (as Bill Mulder): And if you can't appease their conscience you kill them. But you can't kill them all. You can't kill their love, which is what makes them who they are. Makes them better than us. Better than you.
It May Help You on Your Quest: Mulder's mother directs Mulder to look for a device — a spike weapon — for killing green-blooded alien clones. Subverted because he never successfully uses it on an alien.
Manipulative Bastard: The Alien Bounty Hunter is up to his old tricks posing as Jeremiah Smith after he is kidnapped.
The Men in Black: CSM sends a bunch of them to Jeremiah Smith's workplace to kidnap him.
Myth Arc
Oh, Crap!: CSM has a flash of this silent reaction to seeing Jeremiah Smith shapeshift into Deep Throat, CSM's old Syndicate partner who he undoubtedly had murdered.
Pet the Dog: The CSM's concern for Teena seems genuine. Even Mulder more or less takes him at his word on this point. Also Mr X is the one who called an ambulance for her after she had a stroke.
Ungrateful Bastard: X loses his patience after his fight with Mulder and accuses him of being this, after all the help he'd provided thus far.