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That the Prime Directive only applies to pre-warp civilizations.
You're not wrong, but man the Prime Directive would make a whole lot more sense if it did. The commonly misunderstood version of the PD that is intended to prevent cultural contamination is clear and simple. Given its status as the literal top rule, the actual PD—a generalized non-interventionism/pro-isolationism dictum—is oddly complex, vague, and lacking a focused objective.
I still want the story of the one mousey, overworked lieutenant junior grade whose job it is to follow-up on all prime directive violations.
Investigator: Alright, Captain, let's begin, shall we? Apparently you and your crew intervened in a labour dispute between two independent worlds, and taught the previously exploited civilization about unions, and now their entire social development has radically shifted. Is there anything in that basic statement you'd like to dispute?
Captain: Uh...when did this happen?
Investigator: Stardate 43012.7.
Captain: That was eight months ago!
Investigator: Correct. I've had an entire backlog to work my way through, and this is the earliest I was able to address your situation.
Captain: Five months ago my entire ship was trapped in a time vortex and we all deaged to adolescence.
Investigator: ...I did think you looked rather young.
Captain: We don't even have any memory of those events, but it does sound pretty dope. Surely you can't hold us responsible for actions we haven't yet committed, and might not actually commit if we were put into similar circumstances again.All of this could be avoided if they'd just rename it to the Mind Your Own Business Directive.
One of my favorite formulations of the PD comes from an old text adventure game, Star Trek: The Promethan Prophecy: "You can look all you like, but don't touch."
Besides the fact that the Prime Directive is violated constantly, what am I missing about it?
It's about interference with non-Federation governments and cultures in general. The Prime Directive forbids mucking about with Romulan politics, for instance. Worf gets away with a lot of things that would violate the Prime Directive in regards to the Klingon Government because he has dual citizenship and is a member of Klingon nobility.
The ban on contact with pre-warp civilizations is also more specifically uncontacted pre-warp civilizations (you can chat with them if they're already buying Romulan ale from the Ferengi because the damage has already been done) and more generally pre-interstellar civilizations (warp drive is the usual way a civilization becomes interstellar, but there are alternative methods).
Worf gets away with a lot of things that would violate the Prime Directive in regards to the Klingon Government because he has dual citizenship and is a member of Klingon nobility.
Even with Worf being a Klingon, and a recognized member of Klingon society, he still had to resign his commission to leave the Enterprise and go fight for Gowron's forces in the civil war against the Duras' sister's supporters.
Worf: Captain, we must intervene. The Duras family is corrupt and hungry for power with no sense of honour or loyalty. They represent a grave threat to the security of the Federation. Captain, you and I know that they have conspired with Romulans in the past. If they should be victors in this war, they will surely form a new Klingon-Romulan alliance. That would represent a fundamental shift of power in this quadrant. Starfleet must support Gowron. It is in the interests of both the Federation and the Empire. I beg you, support us in our cause.
Picard: Mister Worf, I don't have to lecture you on the principle of non-interference. As Starfleet officers, we have all sworn an oath to uphold that principle whatever our personal feelings. I'm sorry. I must refuse your request.
Picard: Mister Worf. I'm afraid I must recall you to duty. The Enterprise will be leaving this sector immediately.
Worf: Captain, I respectfully request that I be allowed to take an extended leave of absence.
Picard: Mister Worf, your responsibilities as a Starfleet officer are incompatible with remaining on board a Klingon ship during a time of war.
Worf: Captain.
Picard: I order you to return to duty at once.
Worf: Then I resign my commission as a Starfleet officer.They just conveniently forget that's the case in the final scene of "Redemption II" when Worf asks Picard for permission to return to duty. Guess he never got around to filing the paperwork.