Thought of another: In Undertale's Genocide Route, the character you control. It's not often that the villain is the player character, but it is in this case. They even have a boss theme! (At least, that's one interpretation of the music for a certain infamous boss fight.)

I wouldn't even consider the players avatar the villian, but the player themselves.
The game even calls it out for it several times. The players avatar is also nothing an empty husk, but what lies beneath is the true evil. The players drive to see what happens next, which is the sole reason why the genocide run happens, is the true villian. What were your motives to engage in such a run? Both the games creator and the player are to blame (people always forget that the person who made up the situation is the cause as well, the onus isn't solely put on the primary actor alone). Anything else is merely a simulacrum that has no real function other than be controlled.

The best thing about Undertale is that it rewards positivity more, the true good ending is fantastic (most of the game is meh but the things that are amazing really are amazing, unique game).

The Genocide run is very similar in motives and notion as Hotline Miamis final ending, which questions the player motives. You simply want to kill people because you play an action game. You simply want to kill everyone to see what happens and you like the challenge. The small line between interface and the action is more crucial than most people realize. A lot of people who're against the use of millitary drones think that way.

You simply want and it shall happen, that is the nature of the video game regardless of the outcome and the new found understanding that the outcome has bought. Once this crosses the line into reality people may become more pressed to press the big red button while disregarding the potential outcome, if you get what I mean.