Episode: 1x01 | Airdate: Mar 4, 2001
The Lone Gunmen attempt to steal a computer chip, not knowing a thief is watching them. Byers gets bad news and the Gunmen investigate. The investigation leads to a government plot to commit terrorism on American soil.
Episode: 1x02 | Airdate: Mar 11, 2001
The Lone Gunmen are trying to find out who killed a fellow hacker. In the midst of their adventures they meet a not-so-bright football player named Jimmy Bond.
Episode: 1x03 | Airdate: Mar 16, 2001
After the Gunmen receive a tip which could lead them to a female baker who poisoned members of the French Resistance back in World War II, Frohike goes deep undercover as her long lost son.
Episode: 1x04 | Airdate: Mar 18, 2001
The Lone Gunmen and Jimmy search for the long lost water powered car that Frohike saw with his own eyes back in 1962... but they're not the only ones looking.
Episode: 1x05 | Airdate: Mar 23, 2001
A baby is dropped into the lives of the Lone Gunmen as a link between a popular senator running a campaign for re-election and one of his campaign workers who died in a very suspicious accident.
Episode: 1x06 | Airdate: Mar 30, 2001
A man contacts the Lone Gunmen, believing his life has been stolen after being abducted by aliens. They end up getting caught in a love triangle involving a one-eyed stereo salesman, brainwashing, and a wrestling dwarf.
Episode: 1x07 | Airdate: Apr 6, 2001
The Gunmen receive an email for help from a 'slave' subjected to secret government tests, who turns out to be a super-intelligent chimp called Peanuts.
Episode: 1x08 | Airdate: Apr 13, 2001
Byers and Jimmy pose as prisoners on death row in an attempt to prove a man's innocence.
Episode: 1x09 | Airdate: Apr 20, 2001
While recovering in a hospital, Jimmy begins to suspect that his doctor is a wanted killer. Meanwhile, the Gunmen attempt to stop a poacher who kills grizzly bears to sell their gallbladders.
Episode: 1x10 | Airdate: Apr 27, 2001
In an effort to thwart an arms trade at an upcoming tango competition, Yves and Frohike separately go undercover as tango dancers.
Episode: 1x11 | Airdate: May 4, 2001
While investigating the death of Byers' college roommate, the Lone Gunmen find evidence implicating FBI Assistant Director Skinner.
Episode: 1x12 | Airdate: Jun 1, 2001
To solve the murders of two undercover FBI agents, The Lone Gunmen investigate a Chinese spy ring operating out of a television show for kids.
This episode is referred to as a "lost episode" due to it airing three weeks after the show's series finale.
Episode: 1x13 | Airdate: May 11, 2001
The Lone Gunmen team up with "Man in Black" Morris Fletcher to find Yves when she is suspected of being a member of Romeo-61, a secret government organization responsible for decades of major incidents.
Due to this being the series finale and ending on a cliffhanger, the episode's story and the series as a whole were wrapped up in the events of "Jump the Shark", episode 15 of season 9 of The X-Files.