Star Trek: Deep Space Nine introduced Section 31, an organisation which regularly acted in the way you describe the characters from 24. They operated outside official channels and used questionable methods to do whatever was necessary “for the good of the Federation”. The character of Odo criticised it well:
> 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?
DS9 had an actual instance of torture too, but it was a hero being tortured by... half-hero, half anti-hero[0]? Not sure that one led anywhere, beyond being a very disturbing way to do character development.
Section 31 angle is tricky, because the writers unintentionally[1] made them literally save the entire alpha and beta quadrants, and possibly the entire galaxy, from slow-burn genocide. The Dominion was known to systematically subjugate and ultimately eradicate solid life, and other than the Federation Alliance bloc (that prevailed only because of Section 31's bioweapon short-circuiting the war[2]), the only power left in the known galaxy strong enough to resist the Dominion would be... the Borg Collective, which wasn't really that much better[3].
So, as much as I love DS9, I feel the show (and the larger franchise) has so much unintentional depth, that most obvious takes don't work with fans, because they don't survive scrutiny :).
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[0] - The simple tailor was anything but.
[1] - At least as far as I recall, Section 31 were written to be the rotten apples that got revealed and removed by the heroes, in a pretty straightforward way - but IMO, they failed at this, and instead created something more of Deus Ex Realpolitik.
[2] - And a little bit of actual fleet-eating Deus Ex Machina, on the account of having a demi-god in their midst.
[3] - And nobody in or out of universe really wants to talk about what happened to the latter, except the last season of PIC that tacitly acknowledged it in a "blink and you'll miss it" way.
> DS9 had an actual instance of torture too, but it was a hero being tortured by... half-hero, half anti-hero
If you’re talking about Garak torturing Odo, that seems different than the 24 case because in that instance Garak was explicitly working for “the bad guys”. And even so he was doing the torturing reluctantly and only doing so because the alternative was the torturing being done by another operative which wouldn’t restrain themselves. In other words, in that instance the show was explicitly treating torture as bad.
> made them literally save the entire alpha and beta quadrants, and possibly the entire galaxy, from slow-burn genocide.
Technically it wasn’t the disease which defeated the Founders, though I supposed one can argue it debilitated them enough. Even so, despite the results I didn’t feel like the show was necessarily approving of Section 31 (the main characters actively tried to defeat them).
> Technically it wasn’t the disease which defeated the Founders, though I supposed one can argue it debilitated them enough.
It put a countdown clock on their remaining lifespan. Infecting all the Founders simultaneously with a lethal disease made the entire war (that they were very much winning) moot. For the Founders, the entire reason behind the conflict was to ensure their own safety from hypothetical future threats (they were a paranoid bunch); that obviously is not achieved when all Founders are dead, so the entire calculus changes.
That's what I mean by saying that the virus short-circuited the war. It may have been the compassionate and extremely risky act of Odo that, in true Star Trek fashion, changed hearts and minds and got everyone back to the negotiating table, but even without it, the virus would've ended the war within a week or such - leaving alpha and beta quadrants in a bad state (fighting against now feral but still superior Dominion invasion force), but still much better and more survivable than the war itself was.
> Even so, despite the results I didn’t feel like the show was necessarily approving of Section 31 (the main characters actively tried to defeat them).
The show was very much not approving of Section 31; that one was communicated quite clearly. What I'm saying is that, if you ignore what you're being told and look at what you're being shown - the events that happened, not the main characters' opinions on them - it's becomes much harder to paint Section 31 as villains of the story.
I believe this outcome was not intended by the writers; it's just what the whole storyline ended up adding up to.
> Section 31 angle is tricky, because the writers unintentionally[1] made them literally save the entire alpha and beta quadrants, and possibly the entire galaxy, from slow-burn genocide.
I mean, Jack Bauer, too, saved America from all kinds of unspeakable evil by his clever use of torture. I'd say it's not tricky at all. The morally gray "it's bad but we'd be even worse off without it" justification is kind of the point of those narratives.
Yes, but the difference is that Section 31 in DS9 is obviously "the baddies" to the heroes and the audience, and writers meant it to be "the baddies", and everyone in and out of universe was supposed to be appalled at the mutagenic virus subplot, and yet, taken in context of the larger events in the show, Section 31 came out as a light shade of gray instead of black.
It's one thing if them doing their thing was merely convenient, but the rest of the writing in the show converged into a situation where the Federation was under the wall, with no way to talk or shoot their way out of total defeat (and Earth being glassed to make a point). For Star Trek, that's pretty much a franchise-terminating event; they needed to write their way out of that corner - and Section 31 plot basically did that, before they realized it.
AFAIK the writers did not intend Section 31 plot to be posing the question whether any means are justified if the alternative is being exterminated - but it's what they inadvertently ended up doing.
(It's not the only time they hit a problem like this. AFAIR, the episode "Waltz" was made specifically because fans found more depth in the character of Dukat than the writers intended; as such, the whole point of that episode was to drive home that yes, Dukat is just that evil, period.)
> 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?
https://memory-alpha.fandom.com/wiki/Section_31