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 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
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.
"You're also the reason Section 31 exists. Someone has to protect men like you from a universe that doesn't share your sense of right and wrong." --Luther Sloan to Julian Bashir
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. Odo even compared Section 31 to the Cardassian Union's Obsidian Order or the Romulan Star Empire's Tal Shiar. 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.
"Interesting, isn't it? The Federation claims to abhor Section 31's tactics, but when they need the dirty work done, they look the other way. It's a tidy little arrangement, wouldn't you say?"
After the war, Starfleet Intelligence began a serious effort to stamp out Section 31 once and for all. After Julian Bashir and Data managed to delete Uraei Section 31 was exposed.
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.