Star Trek: Section 31

Star Trek: The Next Generation – Rogue was written by Andy Mangels and Michael A. Martin. Martin told Ayers, "Mangels and I worked out our prose collaboration process for the first time with this one. That is, we work out the plot details more or less together until the story makes us happy … Once everyone has signed off on it, Andy and I decide where to put the chapter breaks and agree which of us is to write which chapters. Then we write, trade our chapters, and make editorial suggestions, and struggle to make all the 'joins' between chapters dovetail (think carpentry)."[1]^: 443

Martin continued, "One element of the story that caused some controversy was the portrayal of Lieutenant Hawk, who was first seen in the movie First Contact, as being involved in a same-sex relationship."[1]^: 443 Mangels also said, "A basic tenet of Star Trek is 'Infinite Diversity in Infinite Combinations,' and I found it frustrating and disappointing—not just as an openly gay writer but also as a lifelong fan—that gays and lesbians had almost no representation in the future world of Star Trek. Just as Trek has over the decades been a beacon of hope for millions of minority racial, ethnic, and philosophical groups who have had reason to worry about their future, it seemed only fitting that Trek fans of varying sexual orientations got to share that optimism of a better and more inclusive world."[1]^: 443 Mangles explained, "Like a lot of Trek authors, Mike and I infuse our projects with characters of different sexual orientations, biologies, religions, politics, and personal lives, in the true spirit of Star Trek."

In a 2010 interview with StarTrek.com, Mangels said Rogue links with his other Star Trek novels.[2]

Star Trek: Voyager – Shadow was written by Dean Wesley Smith and Kristine Kathryn Rusch. Smith said, "Taking Section 31 into Voyager was a real challenge. I'm not sure how it came about, but I do remember enjoying working with Marco on it."[1]^: 444

Palmieri noted the challenge was devising a "plausible Section 31 scenario for Voyager, given its distance from the Federation. We hit upon the idea that an agent had been imbedded on the ship specifically for Voyager's mission to the Badlands, … The twist was establishing that [agent] was already deceased by the time Shadow takes place." The action taken by the agent prior to her demise was only then "wreaking havoc on Voyager."[1]^: 444

Star Trek: Section 31 – Cloak was written by S. D. Perry. Perry told Jeff Ayers, "Marco was talking to me about one of his pet projects and I pretty much begged for the original series. I was lucky again."[1]^: 445 The novel elaborated on the "historical events" mentioned in the Voyager episode "The Omega Directive". While writing Cloak, Perry said Star Trek fans are a "seriously discriminating, and although I'm not the sharpest neat-tech-stuff writer, I really want to do justice to the characters as emotional, real people, and I hope that translates."[3]

Star Trek: Deep Space Nine – Abyss was written by David Weddle and Jeffrey Lang. The plot for Abyss was developed by Weddle and Palmieri after the conclusion of Deep Space Nine. Palmieri recalled, “One of the great things about David's involvement in the project was that Abyss was the story that followed up on Avatar," a 2003 duology written by S. D. Perry.[1]^: 445 Weddle was unable to complete the novel due to television writing commitments. To bring the novel to publication on time, Palmieri approached Jeffery Lang. Lang told Ayers, "The writing and publishing process was pretty straightforward: Marco said, 'Here's the outline; can you have the book back to me on Thursday?' Okay, maybe not that short, but we were working on a tight deadline. Since then, I've learned that we're always working on a tight deadline."[1]^: 445 Lang was previously contracted to write Immortal Coil, which was put aside on Palmieri's recommendation.

According to Lang, the novel was lightly edited. Palmieri suggested the holo-ship from Insurrection (1998) being included, an example of what Lang called Marco-isms which began with "‘Hey, you know what would be neat?"[1]^: 445–46

Star Trek: Section 31 – Disavowed was written by David Mack. Mack said Disavowed would be a "spy-thriller-type-thing."[4] The plot would focus on Julian Bashir finding a new "modus vivendi", insinuating himself into Section 31, with the goal of taking down the organization.[5]

The novel includes characters from Mirror Universe alternate reality. The depiction of the Dominion analogue within the Mirror Universe differs from the Dominion encountered during Deep Space Nine's Dominion War arc. The mirror-Founders pursue their manifesto of bringing order to the galaxy via the "absolute rule of law and justice."[6]

Simon & Schuster published the novel as part of the Deep Space Nine relaunch. Cover artist was Tim Bradstreet.[7]

Star Trek: Section 31 – Control was written by David Mack. A direct sequel to Disavowed, Mack explained on his blog that Control would chronicle Bashir's ongoing "shadow war" against Section 31.[8] The titular character is an artificial intelligence deployed by the Federation called Uraei, which has gone rogue. A similar plot is explored in the second season of Star Trek: Discovery.[9] According to Mack, events depicted A Time to Kill (2004) and A Time to Heal (2004) tie directly to the plot of Disavowed and Control.[10]

Mack had requested a blood-red cover to fit the tone of the novel, "which is brutal, tense, violent, and—by the end—genuinely bloody."[11] Mack also said, "It probably won't surprise anyone to learn that I was in a rather angry state of mind when I wrote the outline."[11]