This article contains spoilers for Star Trek: Section 31 and Star Trek: Deep Space Nine.Dr. Julian Bashir is furious. The Chief Medical Officer aboard Federation Starbase Deep Space 9, Bashir has spent the entirety of the season six episode Inquisition being mentally tormented by Luther Sloan, a member of Starfleet Intelligence. Sloan came to DS9 to investigate reports of a senior officer collaborating with the enemy Cardassians, and thinks hes found his man in Bashir. Worse, Bashir begins to question himself, as evidence mounts that he might indeed be the traitor and has wiped his own mind as a protection.But in the final moments of the episode, Sloan reveals his true purpose. He is part of the black ops organization Section 31 and has been testing Bashir in the hopes of recruiting him. Bashir not only rejects Sloans offer, but expresses disgust at the very idea of the organization.You make it sound so ominous, mocks Sloan (played by character actor legend William Sadler).Isnt it? retorts Bashir. Because if what you say to me is true, you function as judge, jury, and executioner, and I think thats too much power for anyone!The stand off between Bashir and Sloan is just one of many the two will have throughout the later seasons of Deep Space Nine, and is just the start of Section 31s involvement in Star Trek media. Yet, after many years and reimaginings, Deep Space Nine remains the only series to do Section 31 right.The Secret HistoryAccording to Sloan, Section 31 is a subset of Starfleet Intelligence designed to search out and identify potential dangers to the Federation and then deal with them quietly. He points out that Section 31 was part of the original Starfleet charter, giving them authority to do their secret work for centuries.Indeed, we get hints of that secret history in entries that followed Deep Space Nine. Enterprise reveals that Malcolm worked for Section 31 before serving under Jonathan Archer on the NX-01. In Discovery, we learn that Section 31 put sleeper agents on the Klingon home world QonoS in season 1 and used an artificial intelligence called Control to assess threats, leading to the major conflict of the series second season. Although it happened in the Kelvin Universe, Star Trek Into Darkness shows Section 31 working during Kirks time, freeing Khan as a defense against the Klingons. The movie Star Trek: Section 31 goes even further to make the division into heroes, borrowing an ill-fitting Suicide Squad premise.These stories all try to integrate Section 31 into the history of Starfleet, totally dismissing the internal debates about whether Starfleet is a science or military organization and firmly establishing it in the latter. Which miss the point of Section 31. The fact of the matter is that TOS, TNG, and DS9 understood Starfleets military trappings as something humanity sought to shed, not something to be embraced, which made Deep Space Nines Section 31 stories thrilling and provocative instead of darkness for the sake of darkness.Extreme MeasuresThe DS9 episode In the Pale Moonlight ends with one of the all-time great Captains monologues, one very different from those delivered by Kirk or Picard. Via personal log, Captain Sisko confesses to all the things he did, and allowed Garak to do, to force the Romulan Star Empire to join the fight against the Dominion. I lied. I cheated. I bribed men to cover the crimes of other men. I am an accessory to murder, he says. But the most damning thing of all I think I can live with it. And if I had to do it all over again I would.Theres so much to admire about the episodes end: the shot of Sisko raising a glass, the fact that he erases the log right after recording it, Avery Brookss powerful oration. But the best thing may be the fact that Sisko describes his ability to live with his actions as damnable. He doesnt take pleasure in the things he did. He regrets them.Join our mailing listGet the best of Den of Geek delivered right to your inbox!That same ethos drives all of the depictions of Section 31 in DS9. After Inquisition, Sloan and Section 31 pop up time and again across the final seasons of the series. They exploit Bashirs medical ethics to gain access to Cardassian officials as part of an assassination plot and even use Odo to spread a genocidal virus to the Founders, the shapeshifting beings who run the Dominion.Within the context of the Dominion War and even of Siskos sins, its easy to understand Section 31s rationale. The Dominion already conquered the entire Gamma Quadrant and has the means to do the same to the Alpha Quadrant. The threat is so great that not even the combined forces of the Federation and the Klingon Empire are enough to stop them. They need the Romulans to stand a chance.And if the Dominion wins, theyll obliterate all the good that the Federation has done. Gone is the spirit of discovery and understanding that the Federation seeks, replaced by the rigid hierarchy and superstition of the Dominion.Which is exactly the point that Sloan makes during his attempt to recruit Bashir in Inquisition. When Bashir charges Section 31 with violating Starfleet principles, Sloan agrees, stating that they do so in order to protect them.Im sorry, but the ends dont always justify the means, says Bashir.Sloan counters, If you knew how many lives weve saved, I think youd agree that the ends do justify the means. Im not afraid of bending the rules every once in a while if the situation warrants it. And I dont think you are either.Despite Sloans logic and charges of hypocrisy against the doctor, who got into Starfleet Medical by lying about his status as an Augment, Bashir disagrees, which is, of course, the point of Inquisition and every Section 31 story that Deep Space Nine told. Times are desperate, and desperate measures seem reasonable. We recognize that but, in the end, we reject them and hold to our values.Sectioning Off Section 31Like the oft-visited Mirror Universe, Section 31 exists as a dark reflection of the Federation. Its not a means unto itself, its not a group that deserves its own stories and characters. It exists to question, and finally to underscore, the importance of the Federation and Starfleet.Nearly every Section 31 story after Deep Space Nine has forgotten this principle (the multiversal version from Lower Decks remains blameless). Theyve gotten too caught up in potential for edgy action, chic anti-heroes in black leather doing the neat stuff all the other cool sci-fi shows get to do. But dystopias always fail in Star Trek and so do dystopian takes on the franchise (seriously, look at the Rotten Tomatoes scores for Section 31).Theres nothing wrong with wondering if the ends justify the means in a Star Trek story, but its no mistake that the only successful Section 31 stories have ended with a resounding No.Star Trek: Deep Space Nine and Section 31 are streaming now on Paramount+.