Let's face it, sometimes your favorite game has you working for the colonialists. Legend of Mana for example has you working with someone who is unambiguously evil. Several people who either want to commit acts of open murder or otherwise.

This isn't about willful decisions to "be the bad guy", your Renegade wheel choices. This is more the idea of the lines that in Mass Effect, you are without a doubt an officer of an organization given supreme power as judge, jury, and executioner.

Etrian Odyssey 1. While the game is better balance-wise than its sequel, it does suffer from the unfortunate issue where you are basically ordered to kill the forest folk, who are like an indiginous people, and you have no choice in the matter.

Drakengard

Oh yes, the part where you drank in the guards was bleak.

Battlefield: Hardline

Yeah that made me uncomfortable too in EO1...

Please explain your replies. Elaboration requested.

It's uncomfortable enough that, if discussing the game (or recommending it) to somebody with a close relationship with an indigineous people (for example, if the person in question belongs to such a tribe), that a trigger warning might be warranted.

Spec Ops: the Line made a big thing about it being your own actions and choice, but honestly, there was no other choice in the game (besides not playing).

I do recall this being a bit infamous as a "feel bad for what you're doing game".

It was feel good about what you're doing, the game until you reach the twist and see exactly what was really happening. Great take on the war genre.

My game:
Greedfall. You're a colonial who has native blood. But you must serve both masters to some degree to complete the game. Also, turning your back on the people who made you what you are, or the people whose blood runs through you, either one is a tough choice to make.

Saints Row 2 is kind of muddied by the fact that while it has anti-capitalist themes, it's ultimately a nihilistic power grabbing crime lord simulator. A fun power fantasy to be sure, but you're pretty much the bad guy fighting equally bad people. Like, you can't even pretend you're good narratively. It's something of a tragic tale if you look at it that way. After that the series basically threw that out in order to become celebrity trash television.

And to add to the discussion of analyzing themes, not necessarily "unfortunate themes", I noticed Soldier of Fortune 2 is basically about fighting a capitalistic terrorist organization. It's not leftist, but you do end up fighting religious fundamentalists, organized criminals, and the terrorists themselves whose goal is to basically extort the world's governments for money. Not putting words in their mouth, but on my end, I think it's because you play as a cop that gets betrayed and has to stop a conspiracy surrounding the privatization of police, only to then be given the keys to the kingdom. Well, kind of inferred, not really elaborated on and probably never will be.

Characters in Dreamfall: Chapters have occasional political rants. "Marxists are good", "Straight people are afraid of gays", "Europe was never white", etc. Sure, previous games were skewed politically too, but Chapters cranked it to eleven, so some dialogs and character behavior don't even make much sense, especially for a fantasy world.

Yes, but that was the purpose of the game

True. Despite that, I still find it very stupid. "you have the choice of not playing" isn't really a good argument, it would be like making a movie praising extremely bad guys and then saying "shame on you for watching, if you didn't you wouldn't feel uncomfrotable". What's even the point then?