As has been pointed out before, the depiction in Discovery of Section 31 as an open, legal organization within Starfleet Intelligence, complete with badges, is at odds with a rogue group unaccountable to anyone in the 24th century. The question is how Section 31 leaves legitimacy and goes rogue and into hiding. I feel the answer might have been provided in "Light and Shadows". If you haven't seen it, stop reading as spoilers are ahead: Spoiler Sarek sends a confused and incoherent Spock to Section 31, over Amanda's objections, believing that they will safely extract the Red Angel info out of Spock's mind and cure him. He does this in good faith and he does not seem to realize that Section 31 has nefarious intentions regarding Spock. However, once Spock is in Section 31 hands, assuming Mirror Georgiou is telling Burnham the truth, then there is no attempt to safely extract info out of Spock's mind. Not even with a mind meld. S31 was going to use a machine to brutally extract Spock's memories and leave his mind permanently damaged. Only Mirror Georgiou's warning to Burnham caused Burnham to break Spock out and get him to safety. At some point, Sarek is going to hear about what Section 31 did. And it's safe to assume that, even with his Vulcan emotional control, he will not be happy to put it mildly. When Spock recovers, while he may understand that Sarek did not know S31 was going to harm him, he may still be disappointed at Sarek's failure of logical deduction to realize S31 was villanous and this may contribute to their lack of communication until TOS, to provide continuity with "Journey to Babel". Being that Sarek is a powerful Federation figure, could he be the one who purges Section 31 from Starfleet Intelligence and sends them into hiding?
I still think trying to weaponize the Talosians' power will have something to do with their downfall.
I'm pretty sure Section 31 is being retconned into "always having been there, you just didn't hear about it because you didn't need to" Hiding? Meh.. Sloan was just being a bit dramatic If they are really "villainous" then they would be disbanded, not forced into hiding. Sarek is going to be Vulcan ambassador for like another 100 years or so. He'd know if Section 31 went into hiding. I doubt Federation would keep Section 31 secret just not to piss off Sarek.
Absolute power corrupts absolutely. We've already got an unstable power dynamic in the form of a tripod: Leland while seemingly having a conscience somewhere deep in his pockets, has shown incredibly poor decision making by allowing a known mirror universe despot and a klingon in human skin into his organization. He's also subject to blackmail. The Empress. She has no loyality to the UFP, hatred towards the Starfleet that forced her here and only a marginal kind of knowingly misdirected motherly feeling to Michael Burnham. Admiral Cornwell. She's advocated a high-risk genocide plan, she's been willing to work with the Empress, she sleeps with people she thinks may be mentally ill (and beneath her in a direct line of command). What little ethics she may have seem to disappear when handed a glass of whisky. She's been manipulated multiple times by multiple people, and she once vaporized a bowl of cookies with a phaser in a crowded room. An organization like Sec.31, as chaotic and dangerous to their parent organizations objectives may be, might still be allowed to exist if they can deliver on their reason for existence. But so far this version of Section 31 has not shown any real victories beyond keeping L'Rell in power a little longer. With mounting enemies like Sarek (admittedly also involved in Cornwall's original plan) , Pike, and poor choices like putting a known murder onboard a ship WITH the person he murdered, I suspect Sec.31 will be given enough rope to hang themselves. What I find interesting is when DID they become more publically known? Archer was the first president of the Federation. he knew about the UE version of Section 31 and was not happy with them at all, for good reason. Perhaps he required enforcement of section 31 of the revised starfleet treaty to at least require oversight, if he couldn't weed it out altogether. Archer was not beyond nefarious acts of his own, and could have seen some value in it.
Actually Mirror Georgiou might be the most stabilizing element in Section 31. She did help free Spock after all. More importantly, she knows the next 10 years of Federation history from the Defiant's computer. Thus she knows how Klingon Federation relations will last until the Treaty of Organia. Even if she tried to change the future she read on the Defiant, she knows she probably will fail. Sarek is not all-knowing. Section 31 can completely break away, pretend to be disbanded, and still exist without him knowing. Sarek didn't even know about a Federation conspiracy to undermine his Khitomer peace efforts in Star Trek 6.
I think many proceed on a false assumption - IE that somehow The Federation Council NEVER knew or authorized "Section 31" because "OMG! Gene's Vision™...Section 31 doesn't fit, so it MUST be a rogue/totally unauthorized organization that the 'paragon of virtue' Federation really knows nothing about..." Yeah, no. From the organization's first 'appearance in the DS9 S6 episode: "Inquisition": http://www.chakoteya.net/DS9/542.htm So, yeah, sorry - if anything Sloan is acting like a current U.S. NSA or British MI-6 operative would..but he openly states he belongs to a Branch of Starfleet Intelligence (showing that yes, Starfleet Intelligence DOES and HAS ALWAYS had "Section 31"; and further: "Section thirty one was part of the original Starfleet charter." So, yeah, the idea that somehow "No one in The Federation knows about/sanctions 'Section 31'..." is fannon. From their first appearance they pretty much were the same as the current NSA or MI-6 (or any other 'Black Ops' style organization.
It isn't fanon. There's reason to believe Sloan was using the outdated 23rd century definition of Section 31 when talking to Bashir (technically accurate, just outdated; i.e. true from a "certain point of view"). Odo himself confirms they are rogue as of the 24th century in 'The Dogs of War': Odo: Interesting, isn't it? The Federation claims to abhor Section Thirty One'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?
Nevertheless, even Captain Sisko didn't know about them. They might not be completely unheard of by his time, but they are certainly mostly unheard of. We're talking about a guy who designed Defiant and was in charge of a station crawling with spies. If it was an organization that wasn't' running totally in the black, he would have known, and should have known.
This is like posting video of Palpatine discussing the legend of Darth Plagueis the Wise. Bad guys can and do lie. BASHIR: We've tried that. We've tried and we tried and all we managed to do was to waste two weeks chasing phantoms from here to Vulcan. You want to face facts? Face this fact. Section Thirty one have managed to stay in the shadows for over three hundred years. They're not going to suddenly come scurrying into the light just because Miles O'Brien and Julian Bashir are on the case! O'BRIEN: Which is why I still say we should take this to Captain Sisko and let him contact Starfleet Intelligence. Maybe they can BASHIR: All that will do is alert Section Thirty One to that fact that we're onto them. And you know what they'll do? They'll go deeper into hiding. probably send someone here to destroy whatever headway I've made. No. No more cloak and dagger games. Science is the answer here. Every puzzle has a solution, every disease a cure. It's just a matter of finding it. Now, if you'll kindly get the hell out of here, I have work to do. Odo: Interesting, isn't it? The Federation claims to abhor Section Thirty One'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? All other dialogue points to S31 as being rogue and not even answering to Starfleet Intelligence as of DS9.
You want what's said on TV? Here it is! (from characters more trustworthy than Sloan. Key lines bolded for emphasis)-- BASHIR: We've tried that. We've tried and we tried and all we managed to do was to waste two weeks chasing phantoms from here to Vulcan. You want to face facts? Face this fact. Section Thirty one have managed to stay in the shadows for over three hundred years. They're not going to suddenly come scurrying into the light just because Miles O'Brien and Julian Bashir are on the case! O'BRIEN: Which is why I still say we should take this to Captain Sisko and let him contact Starfleet Intelligence. Maybe they can BASHIR: All that will do is alert Section Thirty One to that fact that we're onto them. And you know what they'll do? They'll go deeper into hiding. probably send someone here to destroy whatever headway I've made. No. No more cloak and dagger games. Science is the answer here. Every puzzle has a solution, every disease a cure. It's just a matter of finding it. Now, if you'll kindly get the hell out of here, I have work to do. Odo: Interesting, isn't it? The Federation claims to abhor Section Thirty One'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?
But you'd think someone on DS9 would have heard it of it before, right? Obviously, the ret-con on DS9 is that Section 31 was there all along, but even in ENT the organization was pretty down low and not many had heard of it, correct?
Bashir, O'Brien, and Odo were stating their opinions. Section 31 is scary and bad, boohoo. Everyone is entitled to their opinion. What Sloan was stating was a matter of fact. They were founded as part of Federation, they do what needs to be done. They stay down low. Some people know about them, most don't. They have been there from the start. Facts, not opinions.
Here's what Sloan actually says-- SLOAN: Section thirty one was part of the original Starfleet charter. The fact Sloan says "original" hints he's talking about Starfleet's charter as of Archer's time, pre-Federation. If S31 were part of the current Federation Starfleet charter, he'd outright say so and wouldn't use the word "original". Also notes he uses the word was not is. Sloan's line itself which you keep pointing to indicates Section 31 was part of the "old" Starfleet and has nothing to do with current 24th century Federation Starfleet.
Why? Is Sisko a part of Starfleet Intelligence? If not - no, he wouldn't have any need to know. He helped design a ship Starfleet thought would help them fight the Borg. At the same time as that, the ENTIRE FLEET was being rebuilt after the Borg attack in TNG BoBW. Sisko didn't find out about Section 31 until he was involved in a situation they were working on. In intelligence the first rule is: "You don't know until you need to know."
And Klingons were part of Federation. We can all slice and dice what's was said on screen and decide what it really means to us. Heck, it's been going on since '66 and ain't stopping any time soon. Personally I have no issues with Section 31 being an official (if not too well advertised) part of Federation (in 22nd, 23rd, 24th centuries and beyond). If new Section 31 series is good, I say I for one welcome our Section 31 overlords!
But you know they exist. You mentioned several real world examples earlier. You may never meet anyone who works for them but they hire tens of thousands of people, they recruit out of colleges and they are indeed well known, even if what they DO isn't.
They go underground because the plot demands it. And it will likely never be shown because as far as this iteration of Trek is concerned, Section 31 isn't the perhaps-paranoid ramblings of Sloan or an organisation that only exists in shadows, but the legitimate intelligence branch of Starfleet.
For a LONG time no one in the U.S. outside of those who were a part of or interacted with - new of the NSA. My point: There's no evidence "Section 31" ever really surfaced. Those who need to know, know; and afterwards were able to keep the secret. We the audience know BECAUSE "Section 31" is a part of the story. We (the audience) DON'T know who in The Federation knowss of Section 31 beyond the characters the story involves.