SECTION 31

Section 31 is a ultra-clandestine agency inside Starfleet.

Starfleet, of course, is the exploratory and defensive military arm of the United Federation of Planets (UFP), a collection of various sovereign planets joined together for mutual protection and advancement; its two charter member worlds being Earth and Vulcan. While from its inception, the Federation was meant to be an instrument of peace and harmony while at the same time reaching deeper into the unknown space to learn and grow, it was known by some that there would always be unseen threats to the stability of the organization. Most would come from outside, such as the Klingon and Romulan Empires, but some would originate from inside with some unscrupulous individuals and groups wanting to advance their own agendas.

When Starfleet was first formally established by way of the Starfleet Charter at the end of the 2130s, Article 14, Section 31 discussed the need on occasion to bend or suspend the Starfleet regulations in times of extraordinary threat. To that end, a very secretive subgroup inside what would become Starfleet Intelligence was created using as its name that little talked about part of the regulation.

The first recorded acknowledgement of the group comes when on the facility known as Deep Space Nine, its resident doctor, a man named Bashir who is later discovered to be a genetically enhanced individual in violation of Federation law, is suspected further of being under the control of the Dominion (a very nasty and dangerous race from the Gamma Quadrant. His arrest and interrogation is conducted by a team dressed in black uniform who would eventually identify themselves. That team's on-site leader, Sloan, is the first to mention it with, "Let's just say I belong to another branch of Starfleet Intelligence. Our official designation is Section 31. We keep a low profile. Works out better that way for all concerned".

He would go on to explain the purpose of Section 31 with, "We search out and identify potential threats to the Federation, [and once identified] we deal with them". When asked how, he replied, "Quietly".

When Bashir expressed disbelief that Starfleet went along with such methods, he said, "We don't submit reports, or ask approval for specific operations...we are an autonomous department". Later, when trying to recruit a vindicated Bashir, Sloan says somewhat chillingly, "I'll admit it takes exceptional people to do what we do ... people who can sublimate their ambitions to the best interest of the Federation. You violate those principles as a matter of course ... in order to protect them." Later, after Sloan and his team depart, DS9 commander, Captain Sisko, when asked how Federation authorities acted when the matter of Section 31 came up, said, " Starfleet Command doesn't acknowledge its existence, but they don't deny it either".

Note: Wikipedia has a very useful page devoted to this spy organization. The terrific website Memory-Alpha has an extensive list of appearances.

I have read a couple of very interesting treatises on the introduction into the Star Trek canon of an organization whose very nature is so contrary to the tenets of the Federation. The consensus is that it is a bad thing, for the most part, but intriguing.

Most interesting to me is that it did not show up in the official stories told in the entire history of the run of three different Star Trek series: the Original Series, the Animated Series (which to this day I still love), and the Next Generation. It was in the fourth series, and way towards the end of that one as well, that we are told about Section 31.

After that, well, occasionally it is mentioned a bit but otherwise, not so much. Well, in canon, at least. In the non-canonical adventures, sometimes  considered apocryphal, books and comics, it has thrived.

I can understand why. Spy fiction is replete with tales of organizations created specifically to defend beliefs by operating contrary to those same beliefs. Why should Star Trek be exempt?