Section 31, Starfleet's rogue spy arm, involves the starship Enterprise; this endangers a tumultuous world they are visiting. The novel also focuses on Lieutenant Hawk, one of the few openly gay characters in Star Trek.
In Voyages of Imagination, Michael A. Martin remarked on the inspiration for Rogue: "After Andy and I finished our tenure on Marvel's monthly DS9 comic, I discovered that Marco Palmieri was the very same Marco Palmieri I already knew from my previous life in the comics industry. I started an e-mail correspondence with him and set up a meeting between him and Andy at the 1999 San Diego Comicon. That meeting got us an invitation to pitch for the TNG slot in Marco's four-part Section 31 series. So we batted out story treatments, and our third one seemed to work. Marco supplied the title, which guided the story development process, and over a period of a couple months we turned our pitch into a detailed outline and got it approved."
On the controversial subject of the portrayal of Lieutenant Hawk (first seen in Star Trek: First Contact) as being involved in a same-sex relationship, Andy Mangels remarked, "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 reasons 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."