The idea for "Unusual Suspects" arose when the show's producers were faced with a dilemma in August 1997: Fox demanded that they begin production on the fifth season of the show, but series co-stars David Duchovny and Gillian Anderson were still working on "The X-Files" movie in Los Angeles, and would be unavailable until the start of the next month. To solve this problem, the producers decided to write an episode focusing on The Lone Gunmen. Staff writer Vince Gilligan was assigned to pen the episode, and he initially drafted a story involving nanotechnology, which series creator Chris Carter vetoed for fear that it would squander possibly the show's one chance to showcase the Gunmen. Carter then proposed an episode about how The Lone Gunmen came to be. Soon after, Gilligan developed the script, setting it in Baltimore. Duchovny is featured in a few of the episode's scenes, which were shot weeks after the majority of the episode.