Section 31 was the name of an officially-nonexistent clandestine organization within Starfleet Intelligence that claimed to protect the security interests of Starfleet and the Federation.
Little information is available about the activities of the organization. One of its operatives claimed that Section 31 dealt with threats to the Federation that others did not even realize existed and that jeopardized the Federation's very survival. Section 31's actions were autonomous and its existence was neither acknowledged nor denied by Starfleet Command or the Federation Council. Those found guilty of posing a security threat to the Federation were dealt with quietly, as one of its operatives, Luther Sloan, once explained. Section 31 was not accountable to anyone; it did not submit reports to anyone or ask approval for specific operations. As such, it has been described as having granted itself the powers of "judge, jury, and executioner." Under Section 31 credo, to save lives, the ends always justified the means and its operatives were not afraid to bend the rules if the situation warranted it. Section 31's existence was likened to that of the Cardassian Union's Obsidian Order or the Romulan Star Empire's Tal Shiar.
Section 31 had no known physical headquarters or base of operations. A select few were chosen to carry widespread knowledge of their operations. Recruitment of new agents had to be done in secret. One method that Section 31 used to accomplish that involved kidnapping potential agents and testing their loyalty. Section 31's recruitment policy did not allow agents to officially retire from duty, and agents who had long since moved on from the agency could be called upon at any time to carry out a mission.
Origins and 22nd Century Presence
The organization was started by the intelligence program Uraei when it found it could not deal with threats to humanity within the confines of the law. Searching the original Starfleet Charter, Uraei discovered Article 14, Section 31, which allowed for extraordinary measures to be taken in times of extreme threat. Using that article as justification, Uraei created a new covert agency called Section 31 and then began assigning people and resources to the new agency.
At some point before 2151, a young Ensign Malcolm Reed was recruited by Section 31 through former Starfleet Security officer Harris. By the time Reed was posted to the Enterprise NX-01, he was no longer actively involved in covert operations.
However, in late 2154, when Reed was investigating the kidnapping of Doctor Phlox, he was contacted by Harris again. Harris' organization had entered into a secret agreement with Klingon Fleet Admiral Krell, in which Harris facilitated Phlox's forcible transportation to a Klingon colony to help in finding a cure for the Klingon augment virus in exchange for a mutually-beneficial alliance.
Harris ordered Reed to slow down Enterprise's investigation until Phlox could develop a cure. Reed complied, but his tampering was discovered by Captain Jonathan Archer and Commander T'Pol, and Reed was thrown in the brig.
T'Pol reconstructed Reed's communication logs and discovered that he had been in contact with Harris. When confronted with this information, Reed confessed that he had been following Harris' orders. Later, Archer had Reed put him in contact with Harris, and Harris told Archer that, if Phlox was successful, the Klingon Empire would stabilize. An outcome that would be quite favorable for Starfleet. Archer remained suspicious of Harris's motives. After the plague was cured, Harris contacted Reed again, but Reed rebuffed him, saying that he only answered to one commanding officer: Jonathan Archer.
In 2155, Harris agreed to provide intelligence on the Earth-based Human terrorist group Terra Prime to the Enterprise crew when it was discovered that Terra Prime was attempting to disrupt the creation of the Coalition of Planets, and to drive all non-Humans out of Earth's solar system. Harris implied to Reed that this information would come at a price to be exacted at a later time.
Section 31 had a cabal of rogue scientists perform research on creating a stable Omega Molecule, a project that ended badly when the molecule destabalized and made warp travel impossible through the Lantru sector.
In the aftermath of what would come to be known as the Lantru disaster Captain Kirk learned of the existence of Section 31. In a meeting two months later Kirk met with several of his fellow officers to form an organization to oppose Section 31. This organization would later become known as the Kirk Cabal.
24th century operations and the Dominion War
In 2374, Section 31 attempted to recruit the chief medical officer of space station Deep Space 9, Doctor Julian Bashir, after putting him through psychological testing on the holodeck of a ship to which he had been abducted. Subjecting Bashir to an elaborate deception designed to test his loyalty to the Federation, Section 31 operative Luther Sloan presented himself to Bashir as the Deputy Director of Starfleet Internal Affairs, and placed Bashir in a scenario wherein it appeared that he had defected to the Dominion. Eventually, Sloan became convinced of Bashir's loyalty and, citing his genetically engineered background and fascination with spy stories, offered him a position within Section 31.
Bashir, appalled at the thought of an organization that regularly violated the very principles and core values upon which the Federation was founded and which was not accountable to anyone, declined Sloan's offer, although Section 31 continued to regard him as a potential asset. After the agency returned him to Deep Space 9, Bashir alerted the station's senior staff, including his commanding officer, Captain Benjamin Sisko, and Bajoran Militia officers Major Kira Nerys and Constable Odo, of Section 31's existence and its attempt to recruit him. Sisko advised Bashir to accept Section 31's offer to join them should they ask again so Bashir could spy on the organization for Sisko.
In mid-2375, Sloan resurfaced and assigned Bashir to diagnose the health of Koval, Chairman of the Tal Shiar, during an upcoming conference on Romulus.
In the course of his efforts to expose Section 31, Bashir discovered that he had actually been manipulated by Sloan into convincing Romulan Senator Kimara Cretak to access Koval's personal database, on suspicions that Section 31 planned to assassinate Koval. This gave Koval sufficient evidence to have Cretak arrested and charged with treason, which assured his own seat on the powerful Continuing Committee. Bashir learned that Koval was an agent of Section 31 after discovering Starfleet Admiral William Ross' complicity in the scheme.
It seemed Section 31 had been planning for what it regarded as a likely war with the Romulan Star Empire following the Dominion War. The agency projected that the Dominion was likely to end up confined to the Gamma Quadrant with the Cardassian Union occupied and left a shambles, and the Klingon Empire left to spend at least ten years rebuilding from the damage left by the Klingon-Cardassian War, the Federation-Klingon War of 2372 to 2373, and the Dominion War itself. Section 31 regarded Cretak as a potential threat to the Federation in the post-war Alpha Quadrant, as her primary loyalties were to the Star Empire's interests, while Koval could be counted on to influence Romulus in the Federation's favor.
Admiral Ross attempted to defend his actions to Bashir by stating that the high cost of the war justified the extreme measures being taken, but Bashir refused to concede that the ends justified the means. Ross responded by dismissing Bashir from his office and forbidding him from repeating and otherwise acknowledging their conversation.
Later that year, while researching the morphogenic virus which was ravaging the Great Link and Odo, Bashir discovered that Section 31 had actually engineered the disease and deliberately infected Odo during a visit to Starfleet Medical three years previously, in a preemptive attempt to neutralize the threat posed by the Founders and the Dominion. Despite the risk that a cure for the disease might reach the Changelings and thus not only strengthen them but also continue the genocidal war they had initiated, Bashir decided to still pursue the matter and find a cure to help Odo. He lured Sloan to Deep Space 9 with false claims of having developed a cure. Sloan, who was committed to the cause of protecting Federation and Starfleet interests at all costs, committed suicide in an attempt to prevent the cure from being discovered, nearly killing Bashir and Chief Miles O'Brien in the process. Unable to revive him, Bashir and O'Brien used a multitronic engrammatic interpreter to link their minds to Sloan's in order to finally retrieve the information before Sloan's brain injuries rendered him brain dead.
By the early 25th century the existence of Section 31 had been revealed to the public at large 25th century, and most of their agents were made to stand trial. While Section 31 appeared to finally be shut down, some Starfleet officers and Federation citizens were uncertain that the bureau was completely shut down.