What are some games in which the protagonists are actually evil and the characters portrayed as villains are actually good? Bonus points if the writers did this by accident, i.e., they weren't trying to be ironic or edgy but rather they just have a shitty sense of morality and/or terrible writing skills.
The best ironic example I can think of isn't about the protagonist or antagonist, per se, but the Synthesis ending in ME3 is a great example. Tagged as the "good ending" in the code, requires the highest war score to activate, color coded green and in the center of the screen. Yet it's basically just a forced galactic-wide space eugenics program.