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"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?"

Section 31 was an organization which claimed to protect the security interests of United Earth and, later, the United Federation of Planets. During the mid-23rd century, they were considered a critical division of Starfleet Intelligence, while by the 24th century, they were believed to be a rogue organization not considered part of the Federation. (DIS: "Saints of Imperfection"; DS9: "Inquisition", "Inter Arma Enim Silent Leges", "The Dogs of War")

The organization claimed to be sanctioned by the original Starfleet Charter, Article 14, Section 31 of which allowed for extraordinary measures to be taken in times of extreme threat. (DS9: "Inquisition"; ENT: "Divergence")

Section 31 was also somewhat comparable to the Romulan Tal Shiar or Cardassian Obsidian Order except, unlike the latter two, it operated on its own, without Starfleet's knowledge or consent. (DS9: "Inquisition") In the 2250s, it was mentioned in rumors and even had its own insignia that was recognized, a black Starfleet badge. (DIS: "Context Is for Kings", "Point of Light", et al.) By the 2370s, Section 31's very existence was a deeply buried secret, known only to a handful of people beyond its own membership. (DS9: "Inquisition")

Perhaps Section 31's darkest aspect was that, while it had existed since the beginning of Starfleet, it was an autonomous department, 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. (DS9: "When It Rains...") By the time of the Dominion War, at least some of Starfleet Command's top officers knew for certain of Section 31's existence, and on occasion even worked with them to serve the interests of the Federation. However, for the sake of propriety, they tended to keep as much distance from the organization as possible. (DS9: "Inter Arma Enim Silent Leges") As far as Section 31 itself was concerned, it seemed to have well-placed agents in nearly every level of both the civilian Federation government and Starfleet's command structure, allowing it to carry out operations without risk of being publicly exposed. (DS9: "Extreme Measures")

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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. (ENT: "Divergence") 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 Enterprise NX-01, he was no longer actively involved in covert operations.

Klingon Augments

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 Enterprise's brig. (ENT: "Affliction")

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. Captain Archer was very hurt by this revelation at first. Archer told Malcolm that he knew how loyal Malcolm was to the ship and to the captain personally and empathized with him about the extreme difficulty of the quandary he had faced by 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, declaring that he only answered to one commanding officer: Jonathan Archer. (ENT: "Divergence")

Terra Prime

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. (ENT: "Demons", "Terra Prime")

23rd century

Around the 2230s, Section 31 discovered that the Klingons were researching time travel. Believing itself to be in a temporal arms race, the Daedalus Project was developed in the hopes of gaining a strategic advantage. Involved in this project were Leland, and Mike and Gabrielle Burnham. The Burnhams were on the verge of testing a time suit on Doctari Alpha, when it was believed destroyed in a Klingon terror raid. During this period, Section 31 also had at least one operative on Qo'noS. (DIS: "The Red Angel")

By the mid-23rd century, Section 31 operated with some level of oversight from Starfleet. All admirals uploaded reports to Control, an artificial intelligence threat assessment system. They were known to use a black version of the Starfleet insignia which functioned as combadges. (DIS: "Point of Light", "Saints of Imperfection", "Project Daedalus")

During this period, Section 31 was using an abandoned penal colony as its headquarters. The facility also hosted the data center housing Control. (DIS: "Project Daedalus")

Federation-Klingon War

Personnel wearing black badges operated aboard USS Discovery during the first Federation-Klingon War. (DIS: "Context Is for Kings")

Black insignia were seen used aboard Discovery when Michael Burnham first came aboard in " Context Is for Kings ", a fact that was highlighted but went unexplained. Ash Tyler later claimed (in DIS : " Point of Light ") to have heard of the badges but never seen them, suggesting Section 31 was no longer operating on the ship by " Choose Your Pain ", at which point he had joined the vessel's crew. Discovery

Although the Federation did not permit the use of mines, in response to the Klingon use of cloaking devices Section 31 acquired mines built by an outside actor to defend its headquarters. (DIS: "Project Daedalus")

Red Bursts and Control malfunction

After the war, Section 31 operated multiple NCIA-93-type ships. Their leadership included Admiral Patar (a Vulcan and a logic extremist), an Andorian, a Human and a Tellarite admiral. Their operatives included Leland and former Terran emperor Philippa Georgiou. (DIS: "If Memory Serves", "Project Daedalus")

A "bonus scene" deleted from " Will You Take My Hand? " showed the recruitment of Georgiou, in an earlier visit from Leland to Qo'noS, disguised as a Trill. He described his goal as galactic peace and complained that most people were in denial of how dangerous the universe still was despite the Klingon cease fire. He also boasted of being far more resourceful than Starfleet.

In order to ensure stability within the Klingon Empire, Georgiou was sent, on Qo'noS, to protect High Chancellor L'Rell; Georgiou helped her kill Kol-Sha and also fake the deaths of Ash Tyler and their unnamed baby son. Onboard the NCIA-93, Leland and Georgiou recruited Tyler. (DIS: "Point of Light")

At some point following the appearance of a series of red bursts, Section 31 took an interest in finding Spock after he escaped from Starbase 5. (DIS: "Saints of Imperfection")

Eventually, Control took control of Section 31 and killed many of its leaders, including Patar and the other admirals. After the destruction of Section 31 Headquarters, Starfleet ordered all Section 31 ships to search their systems for any evidence of Control. Soon after USS Discovery and NCIA-93 arrived at Essof IV, Leland was captured by Control in order to hijack his body. (DIS: "Project Daedalus", "The Red Angel", "Perpetual Infinity")

Burnham and Spock explored a Section 31 vessel that had delayed a transmission and had been found adrift, with all of its crew except one killed by Control. This was a trap designed to infect Burnham to provide Control access to Sphere data. However, Burnham and Spock managed to kill the remaining crewmember, who had been infected with nanotechnology, and retake the vessel. Soon after, the Discovery was surrounded by thirty-two Section 31 ships, almost all of its fleet, commanded by Control. (DIS: "Such Sweet Sorrow")

After the Discovery was apparently destroyed, Christopher Pike blamed Section 31 for the whole catastrophe. Starfleet Command promised to reform Section 31 to make it more transparent; they named Ash Tyler as its new commander, as both his unique dual existence as Tyler and Voq as well as his rational thinking made him ideal for the job. (DIS: "Such Sweet Sorrow, Part 2")

24th century

Attempted recruitment of 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 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. (DS9: "Inquisition")

Conference on Romulus

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. (DS9: "Inter Arma Enim Silent Leges")

The morphogenic virus

Later that year, while researching the morphogenic virus that 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. Unable to revive him, Bashir and Chief Miles 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. In his mindscape, Sloan attempted to distract Bashir with Section 31's secrets in order to take them with him, but O'Brien got the doctor refocused on their task, and they unlinked their minds from Sloan in time. (DS9: "When It Rains...", "Tacking Into the Wind", "Extreme Measures")

After the cure was discovered, the Federation Council decided against sharing it with the Founders, an act that 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. (DS9: "The Dogs of War", "What You Leave Behind")

Later legacy

By 2380, the existence of Section 31 was no longer a closely held secret. It was sufficiently widely known that Ensign Brad Boimler could claim in a passing remark to Beckett Mariner that Section 31 members speed-walked to conserve energy. (LD: "Envoys")

Alternate reality

In the alternate reality, Section 31 was headed by Admiral Alexander Marcus, 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 SS Botany Bay, with Augments still in cryostasis.

Marcus woke up Khan Noonien Singh, 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 Dreadnought-class vessel, the USS Vengeance, at the Io Facility near Jupiter. He also designed new torpedoes, 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 bombing 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 USS Enterprise to fire the long-range torpedoes on Harrison's location with the Augments still inside. The flagship's warp core was sabotaged, 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. James T. Kirk 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 Montgomery Scott 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. (Star Trek Into Darkness)

Organization and tactics

Is that what we have become? A 24th century Rome, driven by nothing other than the certainty that Caesar can do no wrong?"

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. 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 except within its own echelon; 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." (DS9: "Inquisition") 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 unlike those groups, Section 31 did not instill political dissension or manipulation within the Federation nor did they serve as enforcers in virtute of government policy. 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. This included Captain Benjamin Sisko, who made an inquiry to Starfleet Command that was essentially dismissed. By contrast, both the Obsidian Order and the Tal Shiar showed a willingness to kill anyone even suspected of being a threat, and to them, threats included citizens with opposing views and people who knew too much. (citation needed • edit)

A weapons summary for the advanced long-range torpedo stated that Section 31 "has been granted" special access privileges allowing the withholding of information about its remote stealth capability to the chief engineer. While this was presumably Marcus' handiwork, the language does seem to imply that some of Section 31's actions required seeking some level of cooperation from the Starfleet bureaucracy.

By the 24th century and presumably well before then, 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 this 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. (ENT: "Divergence"; DS9: "Inquisition", "Extreme Measures")

Known assets

Personnel

See: Section 31 personnel

Appendices

Appearances

References

Background information

Section 31 was created by Star Trek: Deep Space Nine 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 "The Maquis, Part II" 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!" (Star Trek: Deep Space Nine Companion, p. 551) Behr further commented, "We need to dig deeper and find out what, indeed, life is like in the twenty-fourth century. Is it this paradise, or are there, as Harold Pinter said, 'Weasels under the coffee table.'" (Star Trek: Deep Space Nine Companion) 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. (AOL chat, 1998)

Incidentally, Deep Space Nine was at the time embroiled in a fierce competition with franchise contender Babylon 5, a science fiction show created by J. Michael Straczynski, which featured striking similarities with Deep Space Nine, and which had led to contemporary to-and-fro accusations of plagiarism as both series were almost simultaneously launched. As it so happened, Babylon 5 had, from its very start, already featured a very similar clandestine organization called Psi Corps. Played by Star Trek: The Original Series alumnus Walter Koenig, one of its main recurrent operatives was Alfred Bester, a character comparable to that of the later-conceived Section 31 Luther Sloane operative, as portrayed by William Sadler.

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 "Inquisition", 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, Ronald D. 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 principled Federation we have known… '? Not yet it doesn't… It's a little early to declare the death of the UFP, folks." (AOL chat, 1998)

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. / Naziesque 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 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." (Star Trek: Deep Space Nine Companion, 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." (Star Trek: Deep Space Nine Companion, p. 661)

Section 31 was originally to have featured in seventh season DS9 installment "Chrysalis". The group was included in an early version of the story that also involved Julian Bashir and genetically engineered characters Jack, Patrick, Lauren, and Sarina being sent on a mission together, and posing as Starfleet officers. (Star Trek: Deep Space Nine Companion, 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 "Inter Arma Enim Silent Leges". (Star Trek: Deep Space Nine Companion, p. 661)

While "When It Rains..." 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) The first draft script of "When It Rains..." suggested that, in addition to Sloan, one of multiple doctors who had conducted a series of scans on Odo at Starfleet Medical (in the timeframe of "Homefront" and "Paradise Lost") had been working for Section 31 and had infected Odo with the virus in order to pass it onto the Founders, though the script didn't disclose which medic it had been. In the original version of "Extreme Measures", however, it was established that Section 31 had recruited Doctor Mora Pol to create the virus, intending to inflict the Founders but not Odo. (Star Trek: Deep Space Nine Companion, p. 692) Echevarria and Ronald D. Moore believed, while writing "The Dogs of War", 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." (Star Trek: The Magazine Volume 1, Issue 17, p. 20)

Ira Behr commented, "Well, without a doubt, the thing I wish we could have used more of was Section 31. We came into that late in the game, and I mean, if we had had an eighth season."[1]

Prior to Section 31's appearance in Star Trek: Enterprise, Series Co-Creator and Executive Producer Rick Berman professed, "I doubt we'll see them on Enterprise." (Star Trek Monthly issue 101, p. 18) 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 "Terra Prime" 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 had managed to stay hidden for "over three hundred years" in "Tacking Into the Wind". 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. (AOL chat, 1999)

It was not until the second season of Discovery that it was firmly established that prime universe Section 31, like their Romulan Tal Shiar and Cardassian Obsidian Order counterparts, also possessed considerable military capabilities as early as the 23rd century. The military capabilities of alternate-reality Section 31 had already been established in Star Trek Into Darkness.

In a "bonus scene" deleted from "Will You Take My Hand?", Leland described his goal as galactic peace, all the while complaining that most people lived in denial of how dangerous the universe was. He believed that peace required vigilance and a moral cost. In this, it mirrored a famous "You can't handle the truth!" speech given at a court-martial by Colonel Nathan R. Jessup (played by Jack Nicholson) in the 1992 film A Few Good Men.

Despite Section 31 appearing in various other Star Trek productions, Ira Behr claimed the DS9 writing staff had rightful ownership of the organization, stating, "I know they used it in a movie, but it's ours. We created it." He also draw a parallel between Section 31 and the "political situation" that was current in the year 2015. (What We Left Behind)

Section 31 was included in a hypothetical Season 8 premiere which the DS9 writing staff devised exclusively for the purposes of including the writing of it in the documentary What We Left Behind. In that story, the organization was now covertly led by Julian Bashir and planned to secretly cause the destruction of Bajoran religion, in order to convince Bajor to finally join the Federation.

All of the Star Trek: Deep Space Nine DVDs feature several "Easter eggs" known as "Section 31 hidden files".

Apocrypha

Novels

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.

Novels published by Pocket Books posit that Section 31 was involved in the theft of the Romulan cloaking device by the USS Enterprise, (TOS: "The Enterprise Incident") the development of the Omega molecule and the subsequent destruction of subspace in the Lantaru sector caused by a disastrous test of the molecule, (VOY: "The Omega Directive") and spying upon Federation civilian attorney Samuel T. Cogley. (TOS: "Court Martial") The fact that Starfleet Admiral Cartwright was established to be a Section 31 agent in the Star Trek: Section 31 novel Cloak suggests the possibility that the Khitomer conspiracy was, from the Federation end, a Section 31 operation.

Encounters with Section 31 have been documented in the novel series Star Trek: Section 31. These stories were largely designed around, and serve to explain or provide background to, certain canon events. In the novels, it is additionally 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 Star Trek: A Time to... 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 Federation President, Min Zife, whom they assassinate.

After the events of the Section 31 novel Cloak, Captain Kirk briefed Starfleet Captains Phil Waterson and Nick Silver and Commodores Aaron Stone and José Mendez on his discoveries and suspicions about Section 31. The five men went on to form 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. The novel established that Tucker was the one who coined the name "Section 31" and that the organization was already aware of the existence of the mirror universe. Also according to the novel, 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. The downfall of Section 31 is further detailed in the novels Disavowed and Control when Trill journalist Ozla Graniv, with assistance from Julian Bashir, Sarina Douglas, Data and Lal publishes an expose about Section 31's activities to the public in 2386. In the novel Available Light, the revelations result in the Federation Security Agency carrying out coordinated arrests against Section 31 operatives and assets across the Galaxy, including Admirals Edward Jellico, Alynna Nechayev, Nakamura, and William Ross; the latter of whom would later be murdered in Federation custody, for their role in the forced removal and subsequent assassination of President Min Zife.

In the Star Trek: Enterprise - Rise of the Federation novel A Choice of Futures, when the United Federation of Planets was founded in 2161 and a unified Starfleet was created, Article 14, Section 31 of the Earth Starfleet charter was copied to the Federation Starfleet charter and allowed Section 31 to continued its activities, but it now protected the interests of the entire Federation.

Video games

In Star Trek: Starfleet Command III, 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. In a now-removed mission, 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 Devidians start haunting the Klingon Neutral Zone, Section 31 assists the player in stopping them, and that same contact later sends them to Nimbus III to locate weapons of mass destruction.

Comics

In a couple of IDW Publishing comics, Section 31 had Captain Kirk test Starfleet's new cloaking device in a Star Trek: Year Four - The Enterprise Experiment story, which followed the events seen in TOS: "The Enterprise Incident". Section 31 also had an operative aboard the Enterprise in Star Trek: Mission's End.

In the Star Trek: Ongoing comic series set in the alternate reality, Section 31 were shown to still be active despite Starfleet's efforts to remove all elements of the organization and they continued to secretly plot to ignite war between the Romulans and Klingons using contingency plans devised by Marcus before his death. However, a few of their agents believed that Marcus' actions had set the organization's work back for years to come. Section 31 also attempted to recruit Hikaru Sulu, whose sister Yuki (β) 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 (β) with Starfleet technology; and following Alexander Marcus' death, convinced the Romulan Empire to begin a war with the Klingons, thus taking the pressure off the Federation after Khan's attack.