(Damn this post turned out way longer than I anticipated. I don't blame anyone for skipping it over.

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This is kind of impossible to choose because some of these individuals or regimes are equally evil, but just in varying degrees. Some never murdered billions, but are still pretty evil (Kivas Fajo) and others wiped out many (Female Founder). I hate to be the irritating moral relativist, but I am presupposing that we are looking at evil through the standards of the Federation?
I guess Dukat would fit that standard considering that he assisted in facilitating a holocaust of the Bajorans and ran an infamous labor "camp" equivalent (Terok Nor). He cheats on his wife and forces Bajoran woman to sleep with him in exchange for protecting their families. Which is putting them in an impossible position. He is vain-driven, egotistical. Dukat feels no remorse for what he did on Bajor, but instead actually feels Bajorans should be
grateful to him. If he could, he would restart the Occupation of Bajor in a heartbeat. Even when he harassed the Federation, his ego built up this phony rivalry between him and Sisko. He felt that his Starfleet adversaries should respect him for being a "worthy adversary". Then he sold out his entire species' freedom and sided with aliens that told Garak that one day all Cardassians would be
dead. He did it so that he could gain ultimate power (although he claimed to do it for Cardassia). Would you look at that? What is good for Cardassia coincides with making him "emperor" of the Cardassian Union and any Alpha Quadrant crumbs left over by the Dominion! When that didn't work out, he manipulated a cult of Bajorans and turned himself into some "prophet". He then sided with the Pah-Wraiths so he could be the "emissary" and consume the entire Alpha Quadrant in flames.
There is an urge to kind of empathize with him because he got so much character development. He was also wonderfully portrayed by Marc Alaimo. He also had much more sympathetic moments than say the Borg Queen or Soren. But Dukat still seems pretty evil. I will say that tons of other "villains" throughout Trek do match him, though. He just happens to be my vote. :P
As for the most evil
regime? Let me preface this by saying I am not trolling or trying to annoy anyone but...
The United Federation of Planets is my vote. The dream that became a reality. Seems oddly...
Orwellian to me. Every human from Earth (I'm not talking about random drifters in space) are all dedicated to the single-minded objective of the betterment of Mankind. This sounds great on paper, but the execution has created an assimilated species without nanoprobes. Even the weird zombie-like tone of voice they drift into when they say "we work to better ourselves...and the rest of humanity..." is just weird. I get that we rid ourselves of vanity, hatred, and various -isms that divide us a species. Wonderful. But is individuality an "ism" that needs to be quashed? Seems like it generally frowned upon and you're meant to be a good little Utopian. Is it dangerous because it can potentially lead to bad emotions/actions? Seems like if you're not onboard with this "let's all get along with the galaxy" mantra, then you're some evil monster (see all the so-called evil admirals through Trek lore).
- I'll grant you that the humans in the 23rd century acted a lot closer to us than the ones in the TNG-era.
Picard lectures Offenhouse that humanity is no longer obsessed with the accumulation of things. The "challenge" is to improve yourself. Whatever that means. But part of the problem with this enlightenment in Trek is it created a wall for our self-improvement. When a species believes they've reached the apex of civilization, they feel they have little to nothing to learn from others. In fact, throughout Trek, humans constantly deride, mock, and thumb their noses at other cultures that remind them a little too much of 21st century humans. They mock Klingons as barbaric, Ferengi as greedy, Romulans as sneaky, Vulcans as boring, etc. Granted they do have those characteristics, "enlightened" humans seem a bit too snobby for my tastes. Tuvok even calls humans out for this in one episode.
They also
enslave A.I. (EMH to mine dilithium?) And were going to rip Data apart. This never made sense. He was sentient enough to join Starfleet, but not sentient enough to have the right to choose his fate?
They "assimilate" worlds too, but they're just more devious about it. Klingons called the Federation a "homo sapiens only club". Yeah...I can see why. It looks like once you're inducted into the Federation family, you get your marching orders from Earth. And they didn't have to fire a single shot. The Terran Empire must be jealous...
They have incredible technology to save billions of "primitive" aliens but opt not to do so because of the Prime Directive. And because they worship that old fallacy that "one day a Hitler or Khan Singh might pop out from the species we saved". Yes...and so could a Leonardo de Vinci, Gandhi, or Cochrane. The Prime Directive is ridiculous and I see why so many SF officers ignore it.
I also noticed there was a...heated...debate on Section 31 being completely separate from the Federation. No they are not. They are an arm of the Federation. They collude with non-members because they understand that Section 31's actions, while dirty, are needed (see Admiral Ross). Bashir tells O'Brien that he counted dozens upon dozens of people that had to have been involved in creating the virus. That means people outside of Section 31 helped, because deep down inside they wanted to stop the Dominion by any means necessary. Notice when this became public, there was no real outcry. AND the Federation Council votes to abet
genocide. Odo calls it a "tidy arrangement". What happened to "enlightenment"? If you argue "that's different, it was war." Ok, fine. Well Section 31 says that all the time too. That they're fighting for the survival of the UFP in every action they make. Yet...they're considered "villains" and the Federation Council is not. Huh.
Their actions with the Maquis? They screwed over those settlers. Even if you argue the settlers should have moved for the greater good, what is to stop the Federation from making them move
again? Settlers poor their blood, sweat, and tears to build a colony and the UFP just swoops in cause of a treaty and forces you to uproot...
Don't even get me started on how they attract all these really screwed up aliens to Earth. While I agree that comes with the territory of exploring the unknown, I do wonder if civilians get a vote on Starfleet's actions or not.
I don't think the UFP is
pure evil in a traditional sense, but they definitely strike me as a group that sacrifices liberty for security. But in this case, they sacrifice their vaunted morals for security. They're kind of scary because often they act under the cloak of being good and noble. That makes it really difficult to combat.
“None are more hopelessly enslaved than those who falsely believe they are free.”