"The Pine Bluff Variant" was based on the idea of Mulder going undercover, a topic that Shiban had wanted to work on for a majority of the fifth season. Shiban argued that the concept worked for the series because the theme of Mulder questioning his beliefs was a major element of the fifth season. The episode was indirectly influenced by the 1963 novel "The Spy Who Came in from the Cold", written by John le Carré. The title is also a reference to the Pine Bluff Arsenal, a real United States military base with stockpiles of chemical weapons.