Section 31
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Section 31 is the official designation of a covert secret police organization in the Star Trek fictional universe, within Starfleet Intelligence, which deals with threats to the security of Earth, and later the United Federation of Planets. Its operating authority stems from an oft-overlooked provision of the Starfleet charter — Article 14, Section 31, from which they derive their name — that makes allowances for bending the rules during times of extraordinary threats. While the original intent may have been to give Starfleet personnel some leeway when it comes to unusual or extreme circumstances, some Starfleet officials have taken it a step further in creating a standing organization able to respond to any threat, preemptively if need be. Section 31 might be compared to the Romulan Tal Shiar or Cardassian Obsidian Order, but operates much more clandestinely and effectively (and, unlike those organizations, does not interfere in the day-to-day lives of Federation citizens).
They defy the principles of the Federation in order to protect them, which is one of the reasons why Section 31 is not officially sanctioned by Starfleet, and even its very existence is not acknowledged openly. But the philosophy of protection at any cost that allows for Section 31 is employed officially by Starfleet in other venues, such as with the ultra-secret "Omega Directive," which gives captains almost unlimited authority to destroy the dangerous omega molecule, including violating Starfleet's Prime Directive of noninterference.
Section 31 deputy director Luther Sloan unsuccessfully tried to recruit Julian Bashir on repeated occasions during the Dominion War.
During the Dominion War, among other questionable actions, they engineered a genocidal virus to exterminate the Founders of the Dominion. They also meddled with Romulan internal politics and were said to have had an agent on the Klingon High Council. They also had operatives working within the upper echelons of Federation politics, including the president's office.
The introduction of Section 31 is considered one of the most controversial additions to Star Trek lore, with many fans of the opinion that its existence goes against the vision of Trek creator Gene Roddenberry. However, the film Star Trek VI: The Undiscovered Country, produced while Roddenberry was still alive, revealed that Starfleet was capable of Section 31-style tactics even during the time of Captain Kirk. Perhaps a sign of these shifting attitudes within Star Trek is the fact that three episodes depicting controversial policies — DS9's "Inquisition," which introduced Section 31, and "In the Pale Moonlight," which featured covert attempts to get the Romulans into the Dominion War, as well as Voyager's "Omega Directive" — all aired within the same two-week span.
Very little of Section 31's history has been revealed in on-screen canon. In the Star Trek Expanded Universe a series of novels were published profiling Section 31 operations with regards to James T. Kirk, Jean-Luc Picard, and the crews of Deep Space Nine and Voyager.
It can be inferred that Roddenbery's vision of the Federation stems from our own Democracy and for years. The addition of Section 31 adds a touch of realism to the Star Trek Universe and especially to the concept of the "Federation". Even in our own democracy, the existence of secret organizations such as the NSA and to some extent, the CIA, proves that in some cases, such organizations are necessary for the functioning of democracy.
It is now known that Section 31 originated prior to the events of Star Trek: Enterprise, which starts in 2151. The NX-01's tactical officer, Malcolm Reed, was somehow involved with the section prior to his posting aboard Enterprise and was recalled to service in November 2154 to prevent Enterprise from interfering in the creation of a viral cure that would also alter Klingon physiology (as detailed in the episodes "Affliction" and "Divergence"). For his role, Reed was thrown into the brig by Captain Jonathan Archer until he explained his actions and revealed his contact, a man named Harris. The next year, during the crisis caused by the Terra Prime terrorist group commandeering a powerful energy emitter used in the terraforming of Mars and using it to hold Starfleet headquarters hostage, Reed went back to Harris for help in finding a way onto Mars past the sensor networks. Harris provided details to flaws and holes in the martian sensor networks that would allow them to infiltrate the base, although he assured Reed that it would not be the last time they met ("Terra Prime").
Fandom conjectures regarding Enterprise and Section 31 have also served to help rectify alleged continuity problems within the Trek universe, the most recent being the suggestion that Section 31 was responsible for covering up the discovery of several Borg drones in 2153 (two centuries before official first contact), an idea supported by the revelation made in the Star Trek: Voyager episode "The Raven" that Starfleet was aware of the Borg's existence years before the first contact detailed in Star Trek: The Next Generation. Similarly, some believe Section 31 is also responsible for the cover-up of the Temporal Cold War although its resolution at the start of Enterprise's fourth season appears to render this speculation moot.