1989. When Susanne Modeski, a chemist working in the Adanced Weapons Facility, tries to expose the conspiracy against the american people she unwittingly participated in, she enlists the help of a certain FCC employee named Byers. The chemical she developed, a compound that creates hallucinations and acute paranoia, was to be used on the public, under the supervision of Mr. X. This will lead to Byers, Frohike, Langly (the future Lone Gunmen) and Mulder meeting for the first time and opening their eyes to conspiracy theories. Mulder hallucinates little green men and Susanne, to Byers' great despair, is taken by X.
A special episode without Scully and little bit of Mulder (Anderson and Duchovny were still in post-production of Fight the Future), entirely in flashback, with the obligatory humor tied to the trio of the Lone Gunmen. Penned by character pro Vince Gilligan.
Susanne Modeski and her project
Susanne was an organic chemist for the "Army Advanced Weapon Facility at White Stone, New Mexico". She worked to develop "the ergotimene-histamine gas, [...] an aerosolized gas which in small doses caused anxiety paranoia in its subject" -- "EH". Mulder gets exposed to it in great (great) doses. Mulder is in shock and has visual and auditory hallucinations: he sees the clean-up men as little green aliens and their voice is distorted. The fact that Mulder's hallucinations are aliens may be a direct effect of the chemical, or special to Mulder's history (even though he's yet to become a believer) -- Susanne might not have designed it especially for alienvision.
Susanne discovers that the DARPA is planning to proceed with an EBO, an "Engineered Biological Operation. Toxic organic agents used on humans", a test in real conditions. The chemical is placed in small doses inside "asthma inhalers" planned to be distributed in the Baltimore-Washington area. Susanne quits, but one can't just leave MK-Ultra. In her file, Byers reads "Security risks are being attenuated. Dr. Modeski's team has been processed and plausible denial constructed." The FBI is fed false information, that she is guilty of murder, to discredit her and to increase the chances of her being found and arrested -- one agency using another. Right after X successfully captures Susanne, the FBI case is closed.
The birth of the Lone Gunmen
When Susanne and her 3 companions try to prevent the EBO, a cleanup team of military police arrives and erases all trace of the chemical and of the secret service agents' bodies. The team is lead by X, who despite his menacing appearance already has some will in him to fight the system: he spares Mulder's life and lets the 3 go with nothing but a big scare. X was set to watch upon another mind-controlling project in 3X23: Wetwired and here he's seen acting in parallel with military personnel (seen clearly only when Byers' FCC co-worker is arrested). This would make X an employee of the DoD, quite possibly of the DIA (Defense Intelligence Agency).
Detective Munch: "Start with your name and birth date."
Byers: "John Fitzgerald Byers, 11/22/63."
Detective Munch: "Seriously."
Byers: "I was named after JFK. Before the assassination, my parents were going to call me Bertram."
Detective Munch: "Lucky you."
Byers: "We at the FCC enjoy forging positive ties with the American public. It's our way of saying 'Communication is just another word for sharing'."
Frohike (about Mulder): "This dude doesn't look so tough."
Susanne: "Look what they did to JFK!"
Byers: "What did they do to JFK?"
Susanne: "Dallas? 1963? Hello?! They want to control every aspect of our lives, from the cradle to the grave. They practically do already."
X: "Sanitize it."
Byers: "That's it? Just trying to intimidate us, to scare us so we'll keep quiet?"
Frohike: "Byers, I swear to God, I'll shoot you myself."
Byers: "It's all true what Susanne said about you people, isn't it? About John F. Kennedy? Dallas?"
X: "I heard it was a lone gunman."
Susanne's last words: "No matter how paranoid you are, you're not paranoid enough. Tell the truth. Reach as many people as you can with it. That's your weapon."
Frohike: "You feeling better?"
Mulder: "Yeah I am, thank you, I just...err...I have these weird ideas in my head that I can't seem to shake."
Frohike: "What kind of ideas?"
Mulder: "Weird ones. [...] What I need from you guys is to tell me what the hell happened last night."
Byers: "You want the truth?"
Mulder: "Yeah, I want the truth."
Byers: "You might want to sit down, this is gonna take a while. The truth is, none of us is safe. Secret elements within the United States government seek to surveil us and control our lives."
Langly: "Tell him about the hotel room Bibles."
Byers: "Yeah, I'm coming to that. Okay, it all started with Susanne Modeski."