In 1989, a SWAT team raids a Baltimore warehouse and finds Agent Fox Mulder in a box, naked and disoriented. Three men are arrested trying to flee the scene; they are revealed to be John Fitzgerald Byers, Melvin Frohike, and Richard Langly, alias the Lone Gunmen. They argue amongst themselves in the holding cell until Byers is taken to be interrogated by Detective John Munch. In a flashback, we learn the story of how the Lone Gunmen began working together and first met Agent Mulder.
Byers, an FCC employee, is attending an electronics convention at which Frohike and Langly are manning different booths, selling stolen cable. A woman passes Byers' booth, attracting his attention; when he pursues her, she introduces herself as Holly and claims that she is in Baltimore trying to get her daughter back from her abusive ex-boyfriend. She persuades Byers to hack into the Department of Defense's computer network, which turns up an encrypted file on Susanne Modeski, whom Holly claims to be her daughter. Mulder passes by Byers' booth shortly afterward; Holly tells Byers that Mulder is her ex-boyfriend. They recruit Frohike to help decrypt the file, and the two men decide instead to simply attack Mulder, but change their minds when he introduces himself as an FBI agent and shows them a photo of Holly, asking if they have seen her.
Byers returns to his booth to see his FCC colleague being wrongfully arrested for hacking into the Defense Department's computer system; Frohike persuades Byers not to turn himself in, and they instead recruit Langly to hack into the FBI's computer system to see why the FBI are after Holly. They learn that Holly is the real Susanne Modeski and is wanted for murder, sabotage, and terrorism at a weapons factory in New Mexico. When they confront her with their discovery, Susanne admits her true identity, but claims she was framed after leaving her job as a research chemist in disgust over government plans to develop a gaseous weapon that induces anxiety and paranoia and is shortly to be tested on civilians in Baltimore. Byers, Frohike, and Langly initially ridicule the idea that the government would knowingly carry out such shady activity, but decrypt the file on her and discover that she is telling the truth, and that the gas is being stored in a Baltimore warehouse.
As the four of them visit the warehouse, Mulder arrives to arrest Susanne, while two other men show up to capture her; they open fire, hitting the gas and triggering an attack of paranoia in Mulder, who strips naked and hides in a box after hallucinating an alien presence. Susanne shoots the attackers and escapes, just as other men arrive, led by Syndicate member X. They quickly clean up the warehouse to remove all trace of the incident while X intimidates Byers, Frohike, and Langly to force their silence. As Byers confronts X over the government's cover-up of the Kennedy assassination (another of Susanne's allegations), X quips, "I heard it was a lone gunman." This becomes the source of the trio's name.
Munch does not believe Byers' story, but Mulder, who has come around from the effects of the gas, confirms it, and the Lone Gunmen are let go. They have a final encounter with Susanne, who has been unable to get the press to believe her story. She urges them to spread the truth about the government's web of deceit for her just as X's men pull up and force her into a car. The trio start by meeting with Mulder to tell him what happened.
- Bait-and-Switch: Just before he is recruited to hack into the FBI mainframe, Langly is sat with several other people around a table in a dimly-lit, smoke-filled room, asking if anyone has the courage to bet $50, implying that he is in a poker game. However, when one of the other players puts up $50, the camera pulls back to reveal that they are really playing Dungeons & Dragons.
- The Cameo: Because the episode is set in Baltimore, Richard Belzer as Lieutenant John Munch crosses over from Homicide: Life on the Street (also set in Baltimore) to interrogate Byers.
- *Cough* Snark *Cough*: In this case, "(cough) Narc (cough)"; as Frohike and Langly argue over which of their bootleg cable switches is better, Langly notices Byers walking past their booths after Modeski and alerts Frohike by coughing while saying "Narc".
- A Day in the Limelight: The Lone Gunmen carry an entire episode for the first time after having only appeared in one or two scenes an episode in their previous appearances.note
- Deadpan Snarker: Detective Munch is as sarcastically deadpan here as he is in Homicide: Life on the Street.Munch: (entering the interrogation room) Detective Munch, Baltimore homicide.
Byers: Did they find her?
Munch: ...and a good evening to you. Sorry, no sign of your mystery lady.
Byers: She is real, the FBI agent saw her.
Munch: Yeah, well, Special Agent... (checks file) Mulder... is currently being held in five point restraints, jabbering like a monkey. The FBI's not talking either. So what I'm looking at here is a warehouse break-in with nothing stolen. A shootout but no guns. Lots of blood but no bodies. And an FBI agent who likes to take off all his clothes and talk about space aliens. (sits down) Fill me in. From the top. Start with your name and birthdate.
Byers: John Fitzgerald Byers, 11/22/63.
Byers: I was named after JFK. Before the assassination, my parents were going to call me Bertram.note
Munch: Lucky you.
- Deliberately Distressed Damsel: Subverted. The audience and the Lone Gunmen think that Susanne is going to turn out to be a psycho preying on people's protective instincts, but she really is a victim.
- DIY Dentistry: After Susanne reads her file, she goes to the bathroom. The Lone Gunmen are surprised to see she has pulled out a tooth. Unknown to her, a tracking device had been placed under that tooth while she was having surgery. She is shown crying and holding ice to her cheek.
- The Dulcinea Effect: Byers falls for Susanne the moment he sees her and then he loves her for always even though they had to part ways.
- Femme Fatale: An attractive blonde shows up with a cock-and-bull sob story about an ex who done her wrong and lures our heroes into a conspiracy investigation...
- Hot Scientist: Introducing Susanne Modeski, a troubled organic chemist. She's a tall and slim blonde and Byers falls for her.
- How We Got Here: The episode begins with the Lone Gunmen being arrested for their perceived role in breaking into the warehouse and assaulting Mulder. Most of the episode is taken up by a flashback showing how they got there as Byers, Frohike, and Langly are each recruited in turn to investigate Susanne Modeski's claim that the government is developing a paranoia-inducing gas to use as a chemical weapon.
- Interrogation Flashback: The episode opens with Detective Munch from Homicide: Life on the Street interrogating Byers as to what happened during a shoot-out at a Baltimore warehouse.
- Line-of-Sight Name: How Susanne comes up with her fake name. Doubles as a possible Shout-Out to The Usual Suspects, where the trope is also present.Susanne: Holly. Nice to meet you.Byers: Holly. Just like the sugar.Susanne: Yeah... just like the sugar.Byers: Funny...
- Malicious Misnaming: Langly repeatedly addresses rival hacker/stolen cable salesman Frohike as "Doohickey" to get under his skin.
- Origins Episode: The episode shows how the Lone Gunmen began working together on investigating conspiracy theories, and how they met the similarly conspiracy-minded Agent Mulder.
- The Picture Came with the Frame: The picture Susanne Modeski has of her "daughter". She's a top organic chemist who worked for the Advanced Weapons Facility and the evil government people are looking for her. She doesn't have a daughter, but she made her up to gain sympathy of the Lone Gunmen.Byers: What about your daughter?Susanne Modeski: I don't have one. I'm sorry...Byers: The photo?Susanne Modeski: It came with the wallet.
- Prison Rape: As the Lone Gunmen are being kept in a holding cell, Frohike snipes that with his long, blond hair, Langly will be the first of them to be traded for cigarettes, an idea he finds hilarious.
- The Reveal: Amongst other things, we learn how the Lone Gunmen got their name: after Byers questions X about the JFK assassination, X states that he heard it was "a lone gunman".
- Shout-Out: The scene in which Susanne arrives just as the Lone Gunmen learn that she is wanted for murder, sabotage, and terrorism, prompting Frohike and Langly to hide behind Byers in single file, is a deliberate homage to a similar scene in The Wizard of Oz in which the Scarecrow, the Tin Woodsman, and the Cowardly Lion hide in single file behind Dorothy.
- Stepford Smiler: Byers is all smiles as he mans the FCC booth at the electronics convention, but it is clear that while he may believe in the message that the FCC's stricter regulations against bootleg cable are being enacted as a public service (hence the slogan on the buttons, "We're YOUR FCC"), he has long since realised that the PR battle he is fighting on behalf of this message is a lost cause.
- Teeth-Clenched Teamwork: At the time they are recruited to hack into government computer networks on Susanne's behalf, the Lone Gunmen can't stand each other. Frohike and Langly are rival stolen cable sellers, and both regard Byers, a government employee who opposes their enterprises, as a "narc". They set aside their differences to act on Susanne's requests, initially out of attraction to her (in Byers' case) and a chance to show off their hacking skills (in Frohike and Langly's cases), and then out of alarm at the discovery that she is telling the truth about the paranoia-inducing gas.
- Who Shot JFK?: "I heard it was a lone gunman."
- Wounded Gazelle Gambit: Justified. Susanne's story about the psycho boyfriend and abducted child is all lies, but she really needs help, and no one would have believed the truth.