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How do you -- if you do at all -- square protagonists who would be the villains in a different genre? What do you do with the crimes they commit? Are all your criminal heroes "thieves with hearts of gold" like Han Solo, or do you indulge in the grittier side of these stories? And if your "heroes" are rough, how do you make the villains stand out?
Just a reminder that we can talk about this without getting into the gory details. I also think we should take care not to make light of real world atrocities. Thanks.
I don't think that I do 'square' it.
I think it's probably safe to say that my view of morality tends to include more nuance than the D&D alignment system. Many of the other games I play don't use such a system. Heck, all things considered, I may -myself- be categorized "evil," based upon the "modern" views of morality that I read on Enworld, given that my background includes some amount of warfare and being trained in combat arms. So
As far as playing a game, I think it depends upon what type of game the group I am with wants to play. If the desire is to play a Four-Colors Supers game (complete with tropes,) "evil" and how the heroes fight against it will likely be very different than a game in which PCs are mercenaries fighting in a war. In the latter, "good" and "evil" might be defined by who pays the most.
At any rate, a "villain" need not be evil. It may simply be someone who has needs/wants/desires that conflict with the Player Characters. PC pirates can just as easily find conflict with a "good" officer of the navy looking to apprehend the PCs; a rival pirate racing to get to a buried treasure first; or a sleazy governor playing both sides by selling them a map but also feeding information to the authorities.
A way to make "villains" standout, even if the PCs are not heroic is to take some inspiration from real life by thinking about how complicated some of your own relationships may be -and then just turn the volume up on dramatization of resulting conflict.
Complicated relationship with a relative, who you may genuinely love, but have a strong disagreement with about a particular issue? That could serve as the basis for an antagonist.
In that particular case, perhaps that antagonist is the sister of one of the PCs, and the conflict is a difference in how they feel the family name ought to be represented within a less-than-good organization.
Alternatively, maybe an antagonist NPC and point of contention for a campaign story could be the former mentor to the PC group; a difference in ideology or conflicting goals lead to a split. Now, the beloved father-figure to the PCs is also against whom they are competing/warring/trying to politically out-maneuver. Perhaps the challenge is trying to best them while still being respectful of who they were/are to you; defeating them without destroying them.
Rarely do interpersonal interactions and relationships fall into clear-cut alignment categories. Recognizing that can offer a lot more complexity to heroes and villains in a story than simply defining everything as "good" or "bad". That's one way that conflict might arise and make a character a "villain" for the PCs.