The Lone Gunmen impersonate three people to get past a facial recognition security system in the episode "All About Yves", and photos of the people they impersonate appear on screen. The pictures are of executive producers Frank Spotnitz (Langly), Vince Gilligan (Frohike), and John Shiban (Byers).
After the series was canceled following the first season finale, an episode of "The X Files" (1993) was dedicated to wrapping up dangling plot lines from the series. In addition to featuring the Gunmen, who made their debut on The X-Files in 1994, the episode featured the return of Jimmy Bond (Stephen Snedden), Morris Fletcher ('Michael McKean'), Yves Adele Harlow (Zuleikha Robinson), and Kimmy the Geek (Jim Fyfe).
In the episode "Cap'n Toby", the series writer "John Gillnitz" is an amalgam of that episode's three writers: John Shiban', Vince Gilligan, and Frank Spotnitz.
The pilot episode, which first aired on March 4, 2001, concerned a terrorist plot to fly a hijacked airplane into the World Trade Center towers.