Star Trek: Discovery has made Section 31 the worst-kept secret in Star Trek. The Federation's clandestine black-ops agency was teased in Star Trek: Discovery season 1, episode 3 "Context is King", but in season 2, the curtain has fallen on the supposedly mysterious agency - all of the main characters now know about it.
Section 31 was introduced in Star Trek: Deep Space Nine and has become that series' most enduring concept. Given how tumultous the Alpha Quadrant is, it makes sense the United Federation of Planets would have its own intelligence agency similar to the Romulans' Tal Shiar and the Cardassians' Obsidian Order. The key difference is that when Section 31 first appeared on DS9, their existence was unknown even to high-ranking Starfleet officers like Captain Sisko. Section 31 operated autonomously and very few people in the Federation had even heard of it. This was also the case in the prequel series Star Trek: Enterprise, set roughly 200 years before DS9 and a century before Star Trek: Discovery.
At the end of Star Trek: Discovery season 1, the Terran Emperor Philippa Georgiou was recruited into Section 31 by Leland. However, in season 2, the black ops division has abandoned any pretense of being a secret agency, at least where the crew of the U.S.S. Discovery are concerned.
Every Major Character on Discovery Knows About Section 31
In Star Trek: Discovery season 2, episode 5 "Saints of Imperfection," Section 31 blatantly announced their existence to the crew of the Discovery. Philippa Georgiou strutted aboard the starship to bring Captain Pike and Michael Burnham face-to-face with Leland via hologram; however, Pike wasn't the least bit surprised about Leland being part of Section 31 and the Enterprise's captain already knew the black ops agency existed. Leland then transfered Section 31's newest recruit, Ash Tyler, to the Discovery and the former Klingon Torchbearer took a spot on the Discovery's bridge - resulting in the ship's entire bridge crew and senior staff now becoming aware of Section 31.
By the end of "Saints of Imperfection," Pike beamed aboard Section 31's cloak-enabled starship to find Admiral Cornwell waiting. She ordered Leland and Pike to work together to find the fugitive Lieutenant Spock and learn the secret of the red signals in space. Suddenly, Section 31 lost their autonomy and are now under orders of Starfleet Command, at least where the search for Spock is concerned. This new development promises a further expanded role for Section 31 in Star Trek: Discovery season 2, but the agency is now hardly a secret. The Discovery has roughly 136 crew members, and because it's a small ship they'll all know about Section 31, especially when Ash Tyler is seen in the common areas sporting his black combadge.
How Will Section 31 Become A Secret Again?
The question going forward is how will Section 31 become a secret again? By DS9's 24th century era, few had ever heard of Section 31 before Luther Sloan attempted to recruit Doctor Julian Bashir during the Dominion War. Afterwards, Bashir informed Captain Sisko and the rest of Deep Space Nine's senior staff of Section 31's existence but the black ops agency still maintained enough plausible deniability to attempt the assassination of the Romulan Tal Shiar's leader. They later tried end the war by attempting genocide against the Dominion's Founders with a morphogenic virus. And yet, even with such acts, Section 31 still wasn't as blatantly out-in-the-open as they are on Star Trek: Discovery where Leland, Georgiou, and Tyler are mingling with Pike and Burnham.
The decades separating DS9 and Star Trek: Discovery help to explain Section 31's return to the shadows by the 24th century, but it's harder to see how their secret doesn't spread in the 23rd century. Somehow, Section 31 has to slink back into the shadows once again in order to maintain their canonical non-existence - despite the crew of the Discovery and L'Rell of the Klingon Empire knowing they exist. Star Trek: Discovery has been trying to fix and explain its breaks of canon in season 2, but it remains to be seen if and how the prequel series can put Section 31's genie back in its bottle.
Star Trek: Discovery streams Thursdays @ 8pm on CBS All Access and internationally the next day on Netflix.