For the most part I agree with Christopher about Section 31. But I don`t think it is that black and white.
From what I could see, his definition of Section 31 doesn`t fit the Section 31 in Enterprise. Trip is not part of a bunch of rogue Starfleet personnel, someone who is on a level of, for example, Sloan.
Two hundred years before the S31 we're talking about. A secretive organization answerable to no one may start out with benevolent intentions, but two centuries without accountability would inevitably turn any organization corrupt. And two centuries spent striving to preserve S31's own secrecy would've inevitably made that become its highest priority, with "Federation security" having become merely a code phrase for "serving Section 31's own interests." Whatever it started out being, it's nothing more than organized crime by the 24th century.
And even in more modern day Star Trek I wouldn`t classify each and every one working for Section 31 as a villain or a terrorist.
Not each and every person working for the Mafia is equally bad as the dons and enforcers, but that doesn't change the fact that the Mafia is a criminal organization.
Section 31 is in the more modern day Star Trek a rogue, illegal organization but when you compare Section 31 with parts of Starfleet Intelligence (I mean especially Nechayev and her “office”), the differences can get blurred. I would like to believe that SI would never go as far as Section 31 goes but nevertheless, they do some dirty and unpleasant work behind the scenes not intended to become public knowledge.
Once more, the absolutely critical difference is that, no matter how "dirty or unpleasant" Starfleet Intelligence's work may sometimes become, SI is
answerable. They work for the government which is elected by the people. That means that a mechanism exists to STOP THEM if they go too far. There is no such mechanism restraining Section 31. And as the eight years of the Bush administration have demonstrated on both a political and economic level, when any body in power is able to operate without oversight, without regulation, without checks on its power, then it will become corrupt, self-serving, and dangerous.
And it is obvious, too, that although there is a lot of condemnation for Section 31, there are high ranking members in Starfleet who support them and sometimes use their services when it is convenient for them.
There were high-ranking members of the US government who supported the use of torture. That doesn't make it any less evil, any less useless as a means of interrogation, or any less a violation of international law. The fact that high-ranking members of Starfleet sanction S31 merely demonstrates that there's a corruption within Starfleet that needs to be expunged.
And I doubt that S31 would've found so much support in Starfleet if it hadn't been for the desperation of the Dominion War. As we saw repeatedly in DS9 and in INS, the war eroded Starfleet's morals, made its officers willing to sanction things they never would've supported normally, things like military coups and forced relocations and other such clearly immoral acts.
If Section 31 would indeed be a terror organization and Starfleet/the Federation blameless, going public would not be such a big problem.
"Terror organization?" Where did that come from? First off, I'm sick of the way the Bushies shortened "terrorism" to "terror," which is simply grammatically inept; terror is an emotion, not a policy. The term is "terrorist organization." A terrorist is someone who attempts to induce terror in a target population as a political or military tactic, as a way of drawing attention to one's cause or making one's enemies too afraid or disheartened to carry on a fight.
And that means, more to the point, that Section 31 can hardly be called a terrorist organization. They aren't trying to induce terror. On the contrary, they're trying to achieve their ends in a way that draws as little attention as possible, exactly the opposite of what terrorists do. It would be more accurate to refer to Section 31 as a criminal conspiracy.
But what happened also damaged the honour of Starfleet, their honesty and reputation. Klingons don`t react well to that. Maybe there would not be an outbreak of a war but a cold war with occasional attacks is definitely a strong possibility.
Now after the Borg attack and the foundation of the Typhon pact, this revelation would even be more dangerous to Starfleet.
Which is exactly why it was a mistake to keep the secret. What Zife, Azernal, and Quafina did at Tezwa wasn't Starfleet's fault, because those men were civilians, officials in the Federation government. If they'd been overtly ousted and punished through the efforts of Starfleet officers, then the Klingons would have no cause for holding Starfleet complicit, since it would've been clear that Starfleet had been victimized too and had acted properly to regain and avenge its honor by defeating those cowardly civilians who had besmirched it.
But by helping cover up the events at Tezwa, Starfleet has just guaranteed that the Klingons will have a negative reaction when the truth inevitably does come out. That's my point: that the coverup makes things worse than honesty would've been, so the rationale behind the coverup is dead wrong. The argument that the coverup is necessary for Federation security is predicated on the premise that the truth can be concealed forever, and that's complete nonsense. In any open society with a free press, it's impossible to keep a secret of that magnitude indefinitely.