(written from a Production point of view)
Star Trek: Section 31 was a four-part series of thematic crossover novels released by Pocket Books in the summer of 2001. The books spanned all four major Trek television tie-in novel series (at that time), including the Original Series, Next Generation, Deep Space Nine, and Voyager.
The common theme among all these books was the influence of the Section 31 agency on each ensemble, such as an early encounter of 31 agents by James T. Kirk in Cloak (written by S.D. Perry), which tells the backstory from VOY: "The Omega Directive" of Dr. Bendes Ketteract and his foolish attempt at harnessing the power of an Omega molecule which destroyed the fabric of subspace throughout the entire Lantaru sector, and the covert operations Section 31 used to foment that situation.
The TNG outing is Rogue (written by Andy Mangels and Michael A. Martin), which features Lt. Hawk (Star Trek: First Contact) as a protagonist, and the revelation that Picard's Academy buddy Cortan Zweller (TNG: "Tapestry") has had a career as a Section 31 agent when the diplomatic incident resulting from the loss of his assigned starship is on the USS Enterprise-E's mission agenda.
The USS Voyager segment is entitled Shadow (written by Dean Wesley Smith and Kristine Kathryn Rusch) and features the revelation that a Section 31 mole has been part of the crew since the beginning of the voyage through the Delta Quadrant.
Finally, the Deep Space 9 station is involved also, in Abyss (written by David Weddle and Jeffrey Lang), a story which continues the ongoing Relaunch series. This particular installment ties in with the ongoing struggle to power the station after the damage in Avatar, and focuses on Doctor Julian Bashir fighting a Section 31 rogue agent who has left the service of the Section. Section 31 had assigned this genetically engineered scientist to create Jem'Hadar for the Section's use. Instead, he uses these Jem'Hadar, who are loyal only to him, to create a new rise of the teachings of Khan Noonien Singh from the Eugenics Wars.