Ira Steven Behr was inspired by a line of dialogue from Deep Space Nine episode "The Maquis" spoken by Commander Benjamin Sisko: "It's easy to be a saint in paradise." Behr said in the 1999 reference companion to the series, "Why is Earth a paradise in the twenty-fourth century? Well, maybe it's because there's someone watching over it and doing the nasty stuff that no one wants to think about.":551 He expressed an interest of exploring what life was really like for those living the fictional 24th century, saying "Is it this paradise, or are there, as Harold Pinter said, 'Weasels under the coffee table'."
The name, Section 31, was taken from the fictional Starfleet Charter: Article 14, Section 31. The article, according to agents, allowed for extraordinary measures to be taken in times of extreme threat. Such measures included malicious sabotage of enemy installations and technology, biological warfare, and preemptive assassination.
According to Ronald D. Moore there was considerable debate on the origin of the organization, in particular on how the organization was formed and how long ago.
Costume designer Bob Blackman chose the black leather costumes worn by Section 31 agents to appear fascistic.:53 Behr had asked for dark black, severe, hostile looking costumes. In Star Trek: The Human Frontier, Michèle and Duncan Barrett explain that Section 31 agents wearing Starfleet uniforms or dressed as Federation citizens further enhanced their role as an organization that is not constrained by ethics.
David Weddle said many fans felt Section 31 betrayed the value system created by Gene Roddenberry, while others were indifferent or intrigued. "Fans would get into these long ethical and political arguments, really struggling with issues like that, which was great to see.":56 Moore replied to criticisms of betrayal saying, "The idea that there's a rogue element within the Federation doing dark deeds outside the normal chain of command is certainly a provocative one."
Actor Jeffrey Combs, who portrayed Weyoun in Deep Space Nine, enjoyed the appearances of Section 31 saying the stories "gave everything a real flair."
Star Trek: Section 31 crossover novel series was inspired by the Deep Space Nine episode "Inquisition". The novels are thematically linked. The series continued with Disavowed (2014) and Control (2017), which share plots and characters with other Deep Space Nine, Typhon Pact, and The Fall, novels. Lt. Roberta Luke, from the Voyager episode "Scientific Method", is introduced as an agent in Shadow (2001).
Star Trek Online is massively multiplayer online role-playing game based on Star Trek. The game has been expanded and updated continuously since its publication in 2010. Updates are organized into Episodes, with each episode further divided into four to seven missions, published weekely. All Section 31 missions are introduced by agent Frank Drake, a character created for the game.