In 1989, the Lone Gunmen meet for the very first time when they assist a woman who claims the government plans to use civilians as guinea pigs in a secret experiment.

In 1989, a SWAT team storms a darkened warehouse, its floors dotted with pools of blood. There the officers encounter a naked, paranoid Mulder lying on the ground. Suddenly, the three Lone Gunmen-Langly, Frohike and Byers-spring from a hiding place and make an unsuccessful bid for freedom. Byers is questioned by Detective Munch, who explains that despite evidence of a bloody shoot-out, and the involvement of a (now delusional) FBI agent, he has few clues about what actually transpired. Byers recounts the events that led up to the warehouse shoot-out.  

As the story unfolds, Byers attends a computer show at a convention center. There he meets a strikingly beautiful woman, "Holly," who claims her psychotic ex-boyfriend kidnapped her daughter. "Holly" gives Byers an Internet address, claiming it is her only hope in locating her child. Byers hacks his way onto government computer, where he types in the name of "Holly's" daughter, Susanne Modeski. The computer opens an encrypted file. Frohike, who mans a nearby booth, agrees to decipher the document.   

When "Holly" notices Mulder walking the convention floor, she identifies him as her ex-boyfriend. Frohike and Byers approach Mulder, only to learn he is an FBI Agent. When "Holly" disappears, Frohike and Byers ask Langly to hack onto the FBI mainframe computer, hoping he can find information on Mulder. Langly successfully cracks the mainframe, and learns that "Holly" is actually Susanne Modeski, who is wanted in connection with the bombing of an FBI lab that left four people dead.     

Modeski locates the threesome inside Byers' motel room. She claims the information contained in her file is fabricated. She admits the story about her daughter was a lie... one she made up in a desperate attempt to have the encrypted file deciphered. She tells the men that the government is plotting an experiment in which the American public will be exposed to a paranoia-inducing gas-one she unwittingly helped develop.     

The encrypted file reveals the address of the warehouse where the paranoia-inducing gas is stored. It also reveals that a surveillance device was attached to Modeski's tooth by her dentist. Using pliers, Modeski extracts a molar containing a tiny transmitter. Byers, Modeski and the others break inside the warehouse. There they discover asthma inhalers containing the gas. Mulder steps forward and announces that everyone is under arrest. Moments later, government officials enter the warehouse and instruct Modeski to follow them. When Mulder orders the men to identify themselves, they open fire, inadvertently striking the asthma inhalers. The liquid rains onto Mulder, triggering a psychotic episode. Modeski shoots the unidentified men and escapes. X steps forward and prepares to kill the threesome execution-style. When X lowers the weapon, Byers realizes he only intended to intimidate them.     

When Byers' finishes his story, Munch dismisses it as fiction. Later, the Lone Gunmen are released from jail when Mulder verifies what transpired. Afterward, the threesome locate Susanne at a newspaper office. She laments that no one believes her story. Moments later, government men usher Modeski away.