Section 31 Section 31 was the name of an officially - nonexistent and autonomous clandestine organization which claimed to protect the security interests of United Earth and , later , the United Federation of Planets . Loosely speaking , it was Starfleet ' s black - ops division , operating separately from and usually without the knowledge of Starfleet Intelligence ( though it often recruited members of Starfleet Intelligence ) . Section 31 was also somewhat comparable to the Romulan Tal Shiar or Cardassian Obsidian Order – unlike these other organizations , however , Section 31 ' s very existence was a deeply buried secret , known only to a handful of people beyond its own membership . ( ) Perhaps Section 31 ' s darkest aspect was that , while it had existed since the beginning of Starfleet , it was practically autonomous , having operated for over two centuries with no oversight or accountability whatsoever , even free to kill those it deemed a threat to Federation interests at its own discretion . ( ) Some high - ranking Starfleet admiral s and intelligence personnel at times seemed to be vaguely aware that Section 31 existed , though giving them only very broad objectives . ( ) At other times , Section 31 appeared to be an outright puppet master to Starfleet , directing the actions and even overall political policies of the Federation itself . ( ) History . 22nd century . The organization ' s title came from the original Starfleet Charter , Article 14 , Section 31 , which allowed for extraordinary measures to be taken in times of extreme threat . ( ) At some point before 2151 , a young Ensign Malcolm Reed was recruited by Section 31 through former Starfleet Security officer . By the time Reed was posted to , 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 , 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 " Enterprise " s brig . ( ) T ' Pol reconstructed Reed ' s communication log s and discovered that he had been in contact with Harris . When confronted with this information , Reed confessed that he had been following Harris ' orders . Captain Archer was very hurt by this revelation at first . Later however , Captain Archer told Malcom that he knew how loyal Malcom was to the ship and to the Captain personally and what an impossible position it must have been for him in having his loyalties divided . 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 ' 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 the Sol system . Harris implied to Reed that this information would come at a price , to be exacted at a later time . ( ) 23rd century ( alternate reality ) . In the alternate reality that split off in 2233 , Section 31 was headed by Admiral , and had a base located beneath the Kelvin Memorial Archive in London . Following the destruction of Vulcan and a subsequent attack that the " Narada " committed against Earth in 2258 , Section 31 began exploring more direct means of defense , particularly against the Klingon Empire . Exploring unknown regions of space , they discovered the , with Augment s still in cryostasis . Marcus woke up , and recruited him into the organization under the pseudonym John Harrison , using his intellect to develop advanced weapons systems . With another seventy - two Augments still in stasis and under Section 31 ' s control , Khan cooperated on a project to build a vessel , the , at the Io Facility near Jupiter . He also designed advanced long - range torpedo es , which he attempted to smuggle his crew in , but his plan was discovered and he was forced to flee . Assuming Marcus made good on his threat to his crew , Khan plotted revenge and blackmailed Thomas Harewood into bomb ing the Archive , before attacking Starfleet Headquarters and then fleeing to Qo ' noS with a portable transwarp beaming device he salvaged from the London base . Marcus attempted to cover - up the conspiracy , while still using the events to his advantage by assigning the to fire the long - range torpedoes on Harrison ' s location with the Augments still inside . The flagship ' s warp core was sabotage d , stranding it at the Neutral Zone , where Klingon patrols would come and attack , giving the Federation a reason to go to war with the Klingons . prevented this when he opted to arrest Khan instead of executing him – learning the truth – and returned to Earth to expose the admiral ' s cooperation with a war criminal . Marcus attempted to destroy the " Enterprise " with the " Vengeance " , but sabotage by and a boarding party of Kirk and Khan further foiled Section 31 ' s machinations . Khan killed the admiral and then crashed the " Vengeance " into Starfleet Headquarters , presumably killing all the Section 31 personnel aboard . A year later , Kirk spoke out against Section 31 ' s agenda at a memorial service for those killed by their attempts to harness Khan ' s mind . ( ) 24th century . 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 was not accountable to anyone and regularly violated the very principles and core values upon which the Federation had been founded , 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 that 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 in 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 Changeling s 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 . ( ) After the cure was discovered , the Federation Council decided against sharing it with the Founders , an act which Odo likened to abetting genocide . The cure was later given to the Female Changeling by Odo as a condition for surrendering her forces and ending the war . These events ruined the organization ' s plan to eradicate the Founders . The Changeling ' s surrender ended the war and allowed the Founders to live . Odo eventually returned to the Great Link to distribute the cure to the rest of the Founders , saving his people . ( ) Organization and tactics . Luther Sloan , a high - ranking member of Section 31 , claimed that the organization 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 . How Section 31 obtained the resources it used for its operations such as free use of a holodeck for a few days to freely test Doctor Bashir ' s loyalty is unknown . But , it can be implied that the organization has contacts in the necessary divisions of the Starfleet infrastructure to access needed resources and equipment . Those found guilty of posing a security threat to the Federation were dealt with quietly , as 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 , Julian Bashir described it 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 . Odo once compared Section 31 to the Cardassian Union ' s Obsidian Order or the Romulan Star Empire ' s Tal Shiar . However , when Sloan thought Bashir was a traitor he extensively tested his hypothesis . When Bashir passed all of his tests Sloan let him go despite Bashir ' s vocal objection to Section 31 ' s existence , and Section 31 took no action to stop Bashir from telling his friends everything he had learned . By contrast , both the Obsidian Order and the Tal Shiar have shown a willingness to kill anyone even suspected of being a threat , and to them threats include citizens with opposition views and people who know too much . Section 31 had no known physical headquarters or base of operations . A select few were chosen to carry widespread knowledge of their activities . 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 . ( ; ) Known agents . Furthermore , Admiral William Ross was known to sympathize with Section 31 to the point of willingly turning a blind eye to their activities . Appendices . Background information . Section 31 was created by Executive Producer Ira Steven Behr , and resulted from his desire to look into the darker aspects of the utopia created by Gene Roddenberry . Behr was inspired by a line of dialogue he had written in where Commander Sisko remarks that " " It ' s easy to be a saint in paradise . " " Behr remarked , " " Why " is " Earth a paradise in the twenty - fourth century ? Well , maybe it ' s because there ' s someone watching over it and doing the nasty stuff that no one wants to think about . Of course it ' s a very complicated issue . Extremely complicated . And those kinds of covert operations usually are wrong ! " " ( " " , p . 551 ) According to Ronald D . Moore , the writing staff had " extended discussions " about the backstory of Section 31 , with much debate about how long the organization was to have existed . On the Internet , the concept of Section 31 was criticized by some fans who saw it as undermining Gene Roddenberry ' s vision . Following the broadcast of DS9 Season 6 entry , David Weddle said about how the viewers reacted to Section 31 , " " There were many that were screaming for our heads over that show , ( saying ) that it betrayed everything that " Star Trek " stands for , and the value system that Gene Roddenberry promoted . Others said that of course the Federation would have to have an organization like this . Fans would get into these long ethical and political arguments , really struggling with issues like that , which was great to see . " " ( " Cinefantastique " , Vol . 30 , No . 9 / 10 , p . 56 ) In response to such criticisms , Ron Moore commented , " " The idea that there ' s a rogue element within the Federation doing dark deeds outside the normal chain of command is certainly a provocative one , I ' ll grant you , but does it really throw into question ' on a fundamental level . . . the principaled Federation we have known . . . ' ? Not yet it doesn ' t . . . It ' s a little early to declare the death of the UFP , folks . " " Costume Designer Bob Blackman noted that the uniforms worn by Section 31 agents were chosen for their fascist overtones . " " We design a lot of Gestapo / S . S / Nazi esque outfits for our villains . And when they ' re really the " ultimate " , like the Section 31 people , we immediately go that way to make them look like storm troopers , because that ' s an imagery that works best , not only for the viewers , but for the producers . For ' Inquisition , ' Ira asked for dark black , severe , hostile looking garments . Well , that ' s black leather . " " ( " " , p . 553 ) In the interim between seasons six and seven of DS9 , the show ' s writing staff determined that bringing Section 31 back in the seventh and final season , delivering on an implicit promise to make the organization return , was an important goal . ( " Cinefantastique " , Vol . 30 , No . 9 / 10 , p . 67 ) " " We ' d had that idea since the end of ' Inquisition ' , " " Ira Behr noted . " " We wanted to bring them back . " " ( " " , p . 661 ) Section 31 was originally to have featured in seventh season DS9 installment . The group was included in an early version of the story that also involved Julian Bashir and genetically engineered characters , Patrick , Lauren , and Sarina being sent on a mission together , and posing as Starfleet officers . ( " " , p . 613 ) The return of Section 31 had to wait until a time when Sloan actor William Sadler was available to appear on DS9 . The very deliberate idea of bringing the organization back to the series eventually led to the writing of season seven entry . ( " " , p . 661 ) While was in development , the revelation that Section 31 was responsible for the morphogenic virus ravaging the Founders was seen as too inconsequential by René Echevarria , who co - wrote the episode ' s story as well as scripting the installment . He , as a result , decided to establish that the organization had also infected Odo with the same virus . ( " Cinefantastique " , Vol . 32 , Nos . 4 / 5 , p . 73 ) In the original version of , it was established that Section 31 had recruited Dr . Mora Pol to create the virus , intending to inflict the Founders but not Odo . ( " " , p . 692 ) Echevarria and Ron Moore believed , while writing , that news of Section 31 ' s involvement in the virus had to be learned by Odo in that episode . ( " Cinefantastique " , Vol . 32 , Nos . 4 / 5 , p . 81 ) Actor Jeffrey Combs enjoyed the appearances of Section 31 on " Star Trek : Deep Space Nine " . In retrospect , he said about the organization , " " I loved it . It gave everything a real flair . " " ( ) Prior to Section 31 ' s appearance in " " , Series Co - Creator and Executive Producer Rick Berman professed , " " I doubt we ' ll see them on " Enterprise . " ( ) While the organization seen in that series was never explicitly referred to as " Section 31 " , production staff have confirmed that it was intended to be the same organization seen on " Deep Space Nine " . ( ENT Season 4 DVD audio commentary ) Harris wears a leather uniform similar to the one worn by Sloan two hundred years later , and refers Captain Archer to " Article 14 , Section 31 " of the Starfleet Charter . This is consistent with Sloan ' s comment that Section 31 was created as part of the " original " Starfleet charter , but not with Bashir ' s statement that Section 31 has managed to stay hidden for " over three hundred years " in . Ronald D . Moore , who wrote the DS9 episode , considered Bashir ' s figure a mistake and stated that it should have been only around two hundred . The figure was later corrected . All of the feature several " Easter eggs " known as " Section 31 hidden files . " Apocrypha . Novels . There are no canon ical references to Section 31 activity during the 23rd century in the prime reality , but the novels published by Pocket Books posit that Section 31 was involved in the theft of the Romulan cloaking device by the , ( ) the development of the Omega molecule and the subsequent destruction of subspace in the Lantaru sector , ( ) and spying upon Federation civilian attorney Samuel T . Cogley . ( ) Starfleet Admiral Lance Cartwright was established to be a Section 31 agent in the novel " Section 31 : Cloak " , suggesting the possibility that the Khitomer conspiracy was , from the Federation end , a Section 31 operation . Although the televised appearances of Section 31 have been limited to " Star Trek : Deep Space Nine " and " Star Trek : Enterprise " , a short series of novels , " " , has also been published , documenting encounters with Section 31 in the other " Star Trek " series . These stories were largely designed around , and serve to explain or provide background to , certain canon events . In the novels , it is revealed that Section 31 : Section 31 is also revealed to be responsible for allowing the Dominion to engage in an infamous massacre of Federation civilians during the war , as part of an attempt to recruit a potential agent , Ethan Locken . Section 31 has also appeared in the " " series . In " A Time to Kill " and " A Time to Heal " by David Mack , it is revealed that Section 31 has a hand in a " coup d ' etat " organized against the President of the United Federation of Planets , Min Zife , whom they assassinate . After the events of the novel " Section 31 : Cloak " , Captain Kirk briefed Starfleet Captains Phil Waterson and Nick Silver and Commodores Aaron Stone and José Mendez of his discoveries and suspicions about Section 31 and the five men formed the " Kirk Cabal " , a secret group designed to oppose Section 31 whenever it was involved in any known activity . The Kirk Cabal was still active as of 2376 , when Elias Vaughn recruited Julian Bashir into its ranks . In the novel " Hollow Men " , Tomas Roeder , a Section 31 agent , learns of the Changeling disease and attempts to leak the information to the Dominion . Roeder failed in his objective and Elim Garak was forced to kill him . In " The Good That Men Do " , by Andy Mangels and Michael A . Martin , Section 31 recruited Commander Charles Tucker III to enter Romulan territory . Also according to " The Good That Men Do " , the existence and activities of Section 31 were exposed to the general public by the early 25th century and its agents were eventually brought to justice for their crimes . The public release of Section 31 ' s files and records ended over 300 years of the bureau ' s illegal and unsanctioned black - ops and infiltration programs . It is implied in " Elusive Salvation " that the name of Section 31 may stem from section 31 of floor B ( asement ) 14 in the Pentagon , which in 1996 housed a secretive unit of the US military dedicated to tracking alien threats . Video games . In " " , in a mission in the Romulan campaign , the player is inspecting the damage to the Unity One starbase . While listening to the Federation - Klingon Alliance broadcasts , one Starfleet officer suggests , " " Why don ' t you ask Section 31 ? " " as to how Starfleet could know if the Unity One scans could detect cloaked Romulan vessels . In the MMO game " Star Trek Online " , Section 31 continues to exist well into 2410 . And despite some transparency among the upper echelons of Starfleet , much of Section 31 ' s operations remain unknown to the majority of the general public . Section 31 tests player characters on a mission in a fashion similar to that of Dr . Julian Bashir . A Section 31 agent also enlists the player ' s aid in several other missions . When Devidian s start haunting the Klingon Neutral Zone , Section 31 assists the player in stopping them . Comics . As with the novels , there are no canonical references to Section 31 in the 23rd century prime reality . However , in a couple of IDW Publishing comics , Section 31 had Captain Kirk test Starfleet ' s new cloaking device in the " " story that followed the events seen in " The Enterprise Incident " . Section 31 also had an operative aboard the " Enterprise " in " " . In the " " comic series set in the alternate reality , Section 31 attempted to recruit , whose sister was already a member ; were revealed to be responsible for Landru ; supported a rebellion on a Klingon - backed planet by supplying Robert April ' s alternate reality counterpart with Starfleet technology ; and following Alexander Marcus ' s death , convinced the Romulan Empire to begin a war with the Klingons , taking the pressure off the Federation after Khan ' s attack .