As Captain Benjamin Lafayette Sisko once said, "it's easy to be a saint in paradise."
The world of Star Trek is full of righteous idealism and a future that features humanity in a far more enlightened state than it is now. Gene Roddenberry's vision of a future where greed, racism, poverty (and on and on) are no longer of any concern is a beautiful one — but a world like that comes at a price.
Paradise doesn't come cheap, and this was the thinking behind Star Trek: Deep Space Nine executive producer Ira Steven Behr's creation of a secret, autonomous entity that operated behind the scenes of the Federation. Section 31 is an organization that does whatever it has to in order to secure the paradise that so many people in the Trek world enjoy. It doesn't matter how many people have to be killed (or how many races have to be exterminated) to get the job done — rest assured, Section 31 will do it. Section 31 is a dark side of the Trek future that Roddenberry would likely have never signed on to, and indeed the concept of this shadow organization has been criticized by some fans for this very reason.
Why does any of this matter right now? It was recently revealed that Section 31 will play a major role in the second season of Star Trek: Discovery. Not only that, it has already been playing a role of sorts. The black badges and (some of) the ethical dilemmas of Discovery Season 1 come directly from Section 31, and there was actually a scene deleted from the season finale that featured one of its agents. In the scene, a Section 31 operative recruits the former Emperor of the Mirror Universe's Terran Empire, Philippa Georgiou. The ethically-deficient mirror captain and Section 31 will get along quite well, and that is a horrifying prospect.
Aside from the Georgiou connection, there's also the notion that the Discovery itself already has members of Section 31 on board. Who they are (aside from the ones with the black badges) and what they are after is anyone's guess, but they'll surely do what Section 31 does best and ramp up the drama and the ethical uncertainty. Star Trek: Discovery already revels in those things, so who knows how far all of it will go once Section 31 is uncovered. Discovering them isn't even the worst part — it's realizing how long they've been manipulating events from behind the scenes.
In case you're unfamiliar with this splinter group that pretty much does whatever it wants in the name of the "greater good," it's time to take a look at why Trek storytellers created the group, as well as go through a chronological rundown of Section 31's greatest hits in the Star Trek canon. Keep your ethics firmly in check; this is gonna be rough.
BORN BY BEHR
The group originally appeared on Deep Space Nine, courtesy of the aforementioned Ira Steven Behr. He talks about the reasons for their creation in the Star Trek: Deep Space Nine Companion.
"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... 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."
Deep Space Nine was the perfect show to explore these ideas because it already excelled in featuring such unsettling themes. The show was awash with weasels under almost every table, and it proved to be quite the radical departure from Star Trek: The Next Generation's "adventures of the week in a floating hotel." We say that with love because TNG certainly had it's fair share of ethical dilemmas, as well.
As DS9 spent most of its seven seasons dealing with a cold war (that then turned into a full-on war), the relevance of Section 31 soon came to the forefront. By the time Section 31 was on the scene and the Dominion War has begun in earnest, bottle episodes about a weird alien board game that made you skip and dance around (the Season 1 episode "Move Along Home") were a thing of the past. Though the story of Section 31 started on DS9, the group's roots in the timeline go back way before the 24th century. Let's go back in time, and we'll work our way back.
Section 31 unexpectedly showed up on the prequel series Enterprise, and we learned in the episode "Divergence" that it's actually a part of the original Starfleet charter — Article 14, Section 31. The addition to the charter allows for extreme measures to be taken in times of extreme threat. Exactly what constitutes a "time of extreme threat" is unknown, and we also don't know who gets to decide which measures are extreme and which are not. It's not a well-crafted addition to the charter, and it is kind of a horrible way for Starfleet to have started.
This story point also makes another dramatic reveal — Section 31 actually predates the Federation charter. The table was built on top of the weasel.
Enterprise also introduced us to our first "operative" from Section 31, Harris. He wore a leathery-black uniform that looked like something a fascist dictator would wear, the standard Section 31 dress. DS9 costume designer Bob Blackman designed the costumes to look like formfitting Nazi-wear, and we guess the style didn't change much over the centuries.
The NX-01 Enterprise's tactical officer, Malcolm Reed, was involved with the group when he was an ensign, but he'd broken those ties by the time he joined Archer's crew. Reed would run into Harris and Section 31 again during the episode "Affliction," where he... deep breath... became involved with the Klingon Augment Virus. That's a whole other discussion, but the short version is that the KAV is the canon reasoning for why Klingon head ridges were not present during the original Star Trek series.
It turned out that Section 31 had an agreement with the Klingons regarding a cure for this virus, and that the Enterprise's Doctor Phlox was needed to find a cure. Complying with orders from Harris, Reed relapsed into his old Section 31 ways and tampered with the Enterprise in order to give the kidnapped Phlox more time to find a cure. Reed was thrown in the brig but was eventually released. Though Harris told Captain Archer that the curing of the KAV would be beneficial to Starfleet, Archer didn't trust him. Reed later renounced his former mentor.
Whatever happens with Section 31 on Star Trek: Discovery would chronologically happen next. We'll obviously know more about this period of Section 31 history when Season 2 is unleashed.
Section 31 is no stranger to the alternate Kelvin timeline! You might be in an alternate Trek reality created by J.J. Abrams, but you are NOT safe from the morally dubious methods of Section 31! Many things were changed in Abrams' alternate branch of Trek history, but Section 31 was not one of them.
The group resurfaced in the film Star Trek Into Darkness, where it's headed by Admiral RoboCop (aka, Admiral Marcus) and puts almost the entirety of the film's plot into motion. With the "do as you please" freedom given to him by Section 31, Admiral RoboCop becomes obsessed with defense, particularly from the Klingons. He has a two-step plan for beating them, which goes like this — Step 1: He finds, defrosts, and tries to control the genetically enhanced warlord Khan Noonien Singh. Step 2: He builds a really, really big ship.
We're not going to go into the full details of what his plans were, but the Enterprise from the Kelvin timeline got intertwined with his machinations and ended up having to clean up his mess. Khan isn't really someone you can control (no matter who plays him), and Admiral RoboCop ends up getting his head crushed. His huge ship crashes into San Francisco Bay, and Khan-berbatch is put back on ice by Dr. McCoy. There was also something about experimental missiles. Thanks to Chris Pine and his crew, the Federation was not taken "into darkness" by Section 31.
SLOAN DEAR, HURRY ALONG NOW
Now we're back to Deep Space Nine, the show Section 31 was actually created for, and where the bulk of its dastardly doings took place.
Though most of the DS9 crew were affected by Section 31's drama, no one was more entrenched than Doctor Julian Bashir. As we find out, the good Doctor is a product of genetic manipulation himself (which was outlawed long ago because of KHAAAAANNNN), and he's also a wannabe spy, which we discover in the holodeck-gone-wrong Bond-riff episode "Our Man Bashir." He regularly lunches with the station's resident tailor/master spy Elim Garak, to boot. He's also the most wide-eyed and idealistic of the crew, so he was a perfect target.
Bashir's first meeting with the group came in the Season 6 episode "Inquisition." The Dominion War was already underway, and the Cardassians had betrayed the entire Alpha Quadrant by joining them. Bashir is put through a series of psychological tests by Luther Sloan, who claims to be from Starfleet Internal Affairs. Played to perfection by the great William Sadler, Sloan eventually reveals that he is a Section 31 operative. Convinced of Bashir's loyalty, Sloan offers him a position in the secret organization, which Bashir (and audiences) had never heard of before.
Doctor "this is where heroes are made" Bashir is disgusted by the mere thought of a group that's accountable to no one and goes against every core value the Federation (and Gene Roddenberry) held. He gave Sloan the ol' High Horse Harry and declined, but Sloan made it pretty plain the group would continue to keep an eye on him. Upon his return to the station, Bashir informs Captain Sisko about the group's existence — Sisko instructs Bashir that if the offer to join them is ever made again, Bashir is to take it. In such a position, he would be able to learn all he can about Section 31 and how it operates.
Sloan and Section 31 popped up again in the Season 7 episode "Inter Arma Enim Silent Leges," where it was involved in manipulating the fate of the Romulan Empire once the Dominion War was over. Using Bashir as a pawn, Section 31 (and Admiral Ross, one of the only non-evil or crazy Trek admirals) managed to take out Romulan Senator Cretak, all because it thought she'd pose a threat to the group when the war (which was still very much going on) was over.
Why is Section 31 already planning for what happens after the war, though? The Federation and its allies are severely outgunned — shouldn't the group be more worried about the Dominion threat that is, you know, still actually happening? Section 31 isn't worried at all, because it had already dealt with the end of the Dominion a couple of seasons prior. How did that happen? It's time to take a look at...
THE WORST THING THAT SECTION 31 HAS EVER DONE
How do you avoid losing a war in one easy step? It's simple — genocide.
That seems to be the thinking of Section 31, anyway. Even if it takes the life of one of your allies (and main characters) in the process, the ends justify the blah blah blah.
Later in the seventh season of DS9, we discover that a horrible virus is affecting the Founders, the shape-shifting rulers of the Dominion. Constable Odo is one of them, but his ties to the crew of DS9 (and the horrible acts of the Founders) caused him to turn his back on them. The Founders (or Changelings) exist as a huge, shiny pool in the Gamma Quadrant, referred to as "the great link." In the link, all of them can merge body, thought, and soul with each other. They can also plan the conquest of the Alpha Quadrant.
Let's be clear — the Founders are not saints. They genetically created drug-dependent soldiers, made war on the Federation, and instilled mass paranoia by spreading and "replacing" certain key characters. General Martok lost an eye because of them, and no, you don't get to just do that without consequences. They make it clear they'll wipe out the Federation, the Klingons, and everyone else we've ever known in the Trek universe. Besides the Borg, the Founders (and the Dominion as a whole) are the greatest threat Trek has ever encountered.
So, a virus is going to wipe out the entire Dominion leadership. Yay! They get what they deserve! Not "yay" at all, though, because the virus is not natural. The virus was manufactured and deliberately given to Odo, with the thinking that at some point he would link with another changeling and pass the virus on. That changeling would eventually merge with the link, and just like that, every Founder has the virus.
Who could be behind such a horrible scheme? It wasn't Harry Mudd.
Yep, Section 31 wasn't worried about the war in the aforementioned episode because it had already manufactured the virus and infected Odo with it when he visited Earth a couple seasons before. The group has spies everywhere, so it would have learned that Odo had done just as planned. The genocide was already in process, so, no, there's no further need to worry about this war... let's get a jump on the next one.
The brilliant and horrible plot falls apart mostly due to Doctor Bashir and the strong bonds of friendship. Because all changelings are affected by the virus, Odo was infected too — he became infected later, as he was the carrier. In trying to desperately cure his friend, Doctor Bashir uncovered the truth about the virus and who was behind it.
In a last-ditch effort to save everyone's favorite shape-shifting security chief, Bashir and his BFF Miles O'Brien lure Agent Sloan to DS9 in the episode "Extreme Measures." Preferring to die rather than give up his secrets, Sloan tries to kill himself — but Bashir manages to keep him alive just enough so he and O'Brien can... go inside of his mind.
Talk about extreme measures! Sloan's mind is a tricky and dangerous place, but they do manage to locate the cure. Bashir's greatest temptation comes when he also sees ALL of Section 31's secrets there for the taking, and the chance to wipe them out (this "thing that has slithered into the heart of the Federation") almost overtakes him. Thankfully, he doesn't take the bait. He and O'Brien survive the strange journey with the cure, and Sloan dies.
It is in studying the cure that Bashir realizes that not only did Section 31 know about the virus and how to cure it, but that Section 31 created it in the first place. When he tells Odo about this, Odo remarks that Starfleet claims to hate Section 31 but always manages to look the other way when some dirty work needs doing. As Odo says, it is "convenient."
As Star Trek: Voyager was separated from Starfleet for almost all of it's run, Section 31 never appeared on that show. That's for the best because with all of the Maquis-Borg-Kazon-Hirogen drama (not to mention Neelix's death cheese), Janeway and company had enough to deal with.
Star Trek: Discovery, on the other hand, is another matter.
What effect will this nefarious group of do-badders have on Michael Burnham and the rest of the crew? What effects has it secretly already had? Section 31 is already a group that will do whatever it thinks needs to be done, whatever the cost — what will happen after it enlists Former Emperor Georgiou, a woman who has proven she holds the same values as Section 31, but a thousand times over?
We don't know, and we won't know until Discovery comes back. But we are shuddering at the thought. The re-emergence of Section 31 promises bad things for the Trek universe, but it also promises a shipload of irresistible drama for us.