Always good to see tom2point0 here, he doesn't show up often enough. I have been listening to REWATCH PODCAST cover THE FLASH (90s series) with pleasure, but I didn't have time to watch the actual show, so I can say nothing other than noting that I continue to enjoy Tom and Cory's banter during my commutes and hikes.
DISCOVERY, however, most definitely does not present the secret origin of Section 31. Their name, Section 31, comes from the original 22nd century Starfleet charter: Article 13, Section 31 allows extraordinary measures against extreme threat. Starfleet and Section 31 pre-date the Federation and DISCOVERY.
Section 31 appeared on ENTERPRISE in the year 2155 as a secret cabal within the United Earth government and Starfleet with Enterprise-armsmaster Malcolm Reed a former member. Given that DISCOVERY takes place in 2256, it's clearly not Section 31's starting point. But this does give me an excuse to talk about Section 31.
The reason the DS9 creators came up with Section 31: they were telling war stories and needed to show that the Federation, like any government, would engage in bloody and covert black-ops missions. But Gene Roddenberry's TNG-era declaration that the future was a perfect world had become so entrenched in the franchise that the writers couldn't overturn it. So they introduced Section 31.
From their debut in "Inquisition":
BASHIR
So, are you going to tell me who
you are? Who you work for?
SLOAN
I would think it's obvious -- the
same people you work for. The
Federation. Starfleet.
BASHIR
You don't expect me to believe
you're with Internal Affairs, do
you?
SLOAN
Of course not. Internal Affairs
is a competent department, but...
limited.
BASHIR
Then what department are you with?
SLOAN
Let's just say I belong to another
branch of Starfleet
Intelligence... our official
designation is Section 31.
BASHIR
Never heard of it.
SLOAN
We keep a low profile. It works
out better that way... for all
concerned.
BASHIR
And what does "Section 31"
do -- aside from kidnapping
Starfleet officers?
SLOAN
We search out and identify
potential dangers to the
Federation.
BASHIR
And once identified?
SLOAN
We deal with them.
BASHIR
How?
SLOAN
Quietly.
BASHIR
So if I had turned out to be a
Dominion agent -- what would've
happened to me?
SLOAN
We wouldn't be standing here
having this conversation.
BASHIR
And Starfleet sanctions what
you're doing?
SLOAN
We don't submit reports or ask for
approval for specific operations,
if that's what you mean. We're an
autonomous department.
BASHIR
Authorized by whom?
SLOAN
Section 31 was part of the
original Starfleet charter.
BASHIR
That was two hundred years ago.
Are you telling me you've been
operating on your own ever since?
Without specific orders?
Accountable to nobody, but
yourselves?
SLOAN
You make it sound so... ominous.
BASHIR
Isn't it? If what you say is
true, you function as judge, jury
and executioner. I'd say that's
too much power for anyone.
SLOAN
I admit it takes exceptional
people to do what we do -- people
who can sublimate their own
ambitions to the best interests of
the Federation.
(a beat)
People like you.
BASHIR
Me?
SLOAN
(nods)
We're on the same team. We
believe in the same principles
that every other Federation
citizen holds dear.
BASHIR
But you violate those principles
as a matter of course.
SLOAN
In order to protect them.
BASHIR
I'm sorry. But the ends don't
always justify the means.
SLOAN
(calmly)
Really? How many lives do you
suppose you've saved in your
medical career?
BASHIR
I don't see what that has to do
with anything.
SLOAN
Hundreds... thousands? Do you
suppose that those people give a
damn that you lied to get into
Starfleet Medical? I doubt it.
Bashir is momentarily thrown by Sloan's argument --
SLOAN
We deal with threats to the
Federation that jeopardize its
very survival. If you knew how
many lives we've saved, I think
you'd agree that the ends do
justify the means.I'm not afraid
of bending the rules every once
in a while -- if the situation warrants
it. And I don't think you are either.
BASHIR
You've got the wrong man, Sloan.
SLOAN
(confident)
I don't think so. In time, you'll
come to agree with me.
With Section 31, DS9 could show the Federation engaging in assassination, fraud, genocide, false flag operations, propaganda, facism, torture, psychological manipulation, violation of civil liberties and sheer ruthlessness -- but because Section 31 was a disavowed branch of Starfleet with no official sanction or existence, the writers left themselves an out. They could say the Federation's hands were clean by putting all the responsibility on Section 31. As seen in "Inquisition":
SISKO
There's no record of a Deputy
Director Sloan anywhere in
Starfleet. As for Section 31...
that's a little more complicated.
Starfleet Command didn't
acknowledge its existence. But
they didn't deny it either.
They simply said they'd look into
it and get back to me.
BASHIR
When?
SISKO
They didn't say.
KIRA
Sounds like a cover-up to me.
BASHIR
Is it possible that the Federation
would condone this kind of
activity?
ODO
Personally, I find it hard to
believe that they wouldn't. Every
other great power has a unit like
Section 31... the Romulans
have the Tal Shiar, the
Cardassians had the Obsidian
Order...
BASHIR
But what would that say about us?
That we're no different than our
enemies? That when push comes to
shove, we're willing to throw away
our principles in order to
survive?
SISKO
I wish I had an answer for you,
Doctor.
Perhaps the greatest Section 31 story (there were only three) is "Inter Arma Enim Silent Leges" where Section 31 manipulates Dr. Bashir into staging an assassination and framing an ambassador to maneuver a more controllable ally onto the political chessboard.
Dr. Bashir figures out the plan and needs Admiral Ross to stop it. Admiral Ross has always been an ally: he's allowed our heroes to skirt rules; he's tacitly encouraged the cast's crazier ideas; he's been the most pleasant and supportive admiral ever seen in STAR TREK.
Ross is Professor Arturo. Ross is Dr. Harry Wells. Ross is Dr. Martin Stein. Ross is Temporal Flux. Ross is Dad. Ross is suddenly debilitated by an illness and unable to help, and Section 31 wins. Later, Bashir confronts Ross, having realized: Ross faked his illness to allow Section 31 to proceed with its plans.
BASHIR
And how long have you worked for
Section 31?
ROSS
I don't.
BASHIR
Just a temporary alliance?
ROSS
Something like that.
BASHIR
And you don't see anything wrong
with what happened?
ROSS
I don't like it. But I've spent
the last year and a half of my
life ordering young men and women
to die. I like that even less.
BASHIR
That's a glib answer. And it's a
cheap way of avoiding the fact
that you've trampled on the very
thing those men and women are out
there dying to protect. Doesn't
that mean anything to you?
ROSS
Inter arma enim silent leges.
BASHIR
"In time of war, the law falls
silent." Cicero. So is that
what we've become -- a twenty-
fourth century Rome? Driven by
nothing more than the certainty
that Caesar can do no wrong?
ROSS
This conversation never happened.
You're dismissed.
Ross didn't kill anyone, didn't frame anyone; he simply chose to do nothing to prevent it and is therefore complicit. That's what makes 31 terrifying.
Despite the writers having left themselves a backdoor to say Section 31 is a rogue agency, it would be reasonable to take the view that Section 31 is the Federation and always has been.
Captain Lorca represents their values rather well. I think Lorca is one of them although there's the possibility that he doesn't know he's one of them. Section 31 has often maneuvered unwitting Starfleet officers into acting on their behalf.
Anyway. DS9's first two Section 31 episodes were great and can be read here:
http://www.st-minutiae.com/resources/scripts/542.txt
http://scifijaz.com/t/565.txt