The nerve-staple function in Sid Meierís Alpha Centauri can lead to this fairly easily. From a gameplay perspective, you click the button, and drone riots go away. You get trade sanctions on you, but you weren't making that much off trade anyway, and besides, it's just for a few turns. It really doesn't amount to much worse than a Strongly Worded Letter. Then you turn around and think: "Nerve-stapling?" What could that mean. And then it hits you: it means exactly what it sounds like. And you just did that to thousands of people.
Don't forget that some of the material implies it has rather nasty lasting side effects, too. E.g. the book title "How to raise a nerve-stapled child".
Michael Ely's book Dragon Sun shows ''exactly what nerve-stapling is in a Body Horror fashion. Once everyone knows that Yang does this to his people and any prisoner they capture in battle, everyone turns against him, ever Deirdre, his former ally.
It should be noted that if you nerve-staple the population of another faction's base that you capture, they will hate you and stay at war with you FOREVER.
The game is full of seemingly innocuous things that become horrifying after the fact, like the Mind-Machine interface technology, or the recycling tanks and research hospitals. This is usually due to the often creepy and revealing quotes that follow them. It's not uncommon for a new player to finish building something at one of their bases, or discover a new technology, and think nothing of it, only to go "Wait. What did I just do? What did I just do?" after listening to the corresponding quote.
The factions do represent traditional civilizations, and the leaders are a blatant tell.
The Human Hive = China. Communism, Confucianism and Buddhism all uphold selflessness and unity. Yang took it to extreme by neglecting everything else. Their main weakness being that the people is being held back by the lack of political freedom (negative economic ranking), but that is counter balanced with a hard-working and fast growing population.
Additionally, Yang's given name Sheng-ji can mean "upgrade" in Mandarin Chinese with the appropriate tones, which ties in very well with his obsession over transcendence.
UN Peacekeepers = Modern India. Largest democracy in the world comprised of unified states, home to many religions and languages, favors mental pursuits. But with an infamously sluggish civilian bureaucracy.
Alternatively, Progressive/Liberal USA. Promotes the ideals of democracy and freedom, celebrates cultural diversity and seek to get other nations to work together. But occasionally can a but too enthusiastic in intervening in the internal affairs of other countries or outright launching 'police actions' against them in the name of defending human rights.
Or the European Union - pro-democracy and extremely pro-human rights, as well as international consensus and co-operation - alongside a ton of bureaucracy and inefficiency.
University of Planet = Soviet Union/Russia. Advanced science and powerful technology. But human rights tend to be optional.
Lord's Believers = Fundamentalist USA. Obvious, considering mega churches, creationist museums and Jesus camp. Highly suspicious of technological advances and is largrly view as a pariah by other nations. But extremely powerful militarily.
Gaia's Stepdaughters = European Union. Has more ecologically sustainable policies than anyone else at the expense of actual economy. Mainly rule with a democratic socialist ideology and has plenty women leaders. But also have a dark side of a history full of wartime atrocities.
Morgan industries = African Union. Who would be more focused on wealth than the recently poor? Blood Diamond writ large.
Alternatively, Corporate USA. Strong emphasis on economics. Staunchly capitalist. At least nominally Free-Market, though more on Mega Corp.. Limited to no government. But is also interested in becoming the defacto government of the entire world.
Spartan federation = Latin American Union. Juntas, revolutionaries, cartels, gangsters, police, kidnapers and private security - everyone is armed.
Alternatively, Conservative USA. Encourage and promotes values such as discipline, loyalty, and self-dertermination. Highly suspicious of foreign powers and in responds have a massive 'defense' budget and all citizens being given the right to bare arms. View by outsiders as aggressive and violent. But see themselves as the Only Sane Man in a dangerous and hostile world.
Continuing from the post above, the same goes for the human factions introduced in the Alien Crossfire expansion pack, but instead of established nations, they represent vocal ideological groups that have yet to take power in real life.
Free Drones = Social Democrats. Believe in the idea of eventually achieving a functional workers paradise by working towards a Eudaimonic society. But unlike Stalinism (or the Human Hive), they have not problem with getting power though democratic means or by employing free market economies. Lack the funding or backing compared to other political groups (slow research), but can level the playing field by easily rallying popular support.
Data Angels = Minarchist Libertarians. See government as something that is necessary but only in a very limited manner (democracy as the closest equivalent to their ideals), which makes some people mistake them for being outright anarchists. Look down upon the idea of a large military spending for national defense, but encourage individual initiative in taking action. Also, expand their influence by spreading their propaganda and reaching out to others via the Internet (the planetary network).
Cybernetic Consciousness = Utilitarians. The greatest amount of benefit to the largest amount of people, meaning that the moral worth of an action is determined only by its resulting outcome. Therefore the sacrifice of individuality and emotions is justified by all the resulting benefits of a cybernetic society.
Nautilus Pirates = Anarchists. Svensgaard "leads" them in the sense that he's got the most individual power, but the pirates are intent upon gaining as much wealth and power for as much of their faction as possible. Otherwise, anything goes. Are able to exist as an entity because of the extreme advantage they have over other factions concerning Planet's oceans.
Cult of Planet = Combines Transhumanism with Voluntary Extinctionism. The Cult seeks to remove humanity as an entity one way or another, and it's implied that if they can't Transcend after destroying the other factions that they'll wipe themselves out in order to let Planet exist free of human influence. However, as Planet is doomed to an endless cycle of awakening and withering without humanity's help; it follows that the option of Transcending to save both Humanity and Planet is the preferred outcome.