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Mulder receives a tape containing encoded information about alien visitations, which leads him and Scully to New Mexico.
- Anyone Can Die: Mulder's father, after promising to tell Mulder the truth, is murdered. This reinforces the standards of death in this show, along the same vein as Deep Throat's.
- Badass Bureaucrat: Despite Mulder opening their fight by sucker punching him, Skinner quickly turns the tables and takes Mulder out with a chokehold, though with the assistance of an intervening agent.
- Creator Cameo: Chris Carter makes a quick appearance in Skinner's office as a FBI agent.
- Establishing Character Moment: The Thinker is introduced reading a book called the 50 Greatest Conspiracies Of All Time.
- Fiery Coverup: The Cigarette Smoking Man orders soldiers to burn down a boxcar with hybrid alien bodies. Mulder was inside of said boxcar as well, although his fate is not confirmed.
- Hollywood Hacking: Somewhat averted in that the hacker is seen waiting for his program to do the actual hacking, seemingly having been there a while, as opposed to the instant access typing usually seen on TV.
- Intoxication Ensues: Mulder's water is drugged, causing him to become angry and irrational.
- Magical Native American: Subverted, as Scully contacts Albert Hosteen to help them to translate the Navajo code. Played straight when Albert receives omens from the desert.
- Mr. Fanservice: Shirtless Mulder in his underpants after Scully took him back to her home to recuperate.
- Myth Arc
- Not Himself: Mulder is uncharacteristically violent, confrontational, and aggressive; incidentally, his elderly neighbour also inexplicably kills her husband of fifty years. It turns out their building's water supply was being drugged, to put Mulder in such a dangerous and unstable state of mind that he could be convincingly framed for killing his father.
- Our Hero Is Dead: Mulder is presumed dead after being caught in a boxcar fire. But is he really?
- Percussive Prevention: Sometimes characters help their friends by punching them unconscious. Scully takes it Up to Eleven when she shoots Mulder to prevent him from killing Krycek.
- Percussive Therapy: Mulder, enraged that he got yet another fake instead of top secret information, smashes a pencil holder against the wall in his office. The files were actually encrypted, not gibberish.
- Shirtless Scene: Mulder, who has a bullet wound in his shoulder and is recovering in the motel.
- Super Cell Reception: Mulder makes a cell phone call, while stranded in the middle of a desert inside a boxcar buried underground.
- To Be Continued: Two parts to go, and the Myth Arc is getting thicker.
- Undressing the Unconscious: After his father is seemingly murdered, Mulder goes to Scully's apartment and quickly passes out as she gets him into her bed (Scully later finds out he was being drugged). When he next wakes up, he's only wearing his underpants. He finds his clothes nearby but notices Scully has taken his gun while he slept.
- Water Source Tampering: The Syndicate puts LSD or a similar drug into Mulder's water supply, causing erratic behaviour that discredits both him and the case he is currently following. And since it wasn't just Mulder's water supply, but his entire apartment building's, it also caused at least one murder there.
- Wham Episode: Mulder's father is killed by Krycek, Scully finds out more about her abduction and Mulder is presumed dead by a boxcar explosion after he found alien corpses with smallpox vaccination scars.
- You Killed My Father: Krycek kills Mulder's father and tries to frame Mulder. Scully averts the actual revenge because if she hadn't stopped Mulder from killing Krycek, Mulder would have been found guilty.