For me, it would be GLaDOS.
Portal 2 spoiler
She deleted the one remaining human part of herself because it was just too much to deal with. She releases you at the end of Portal 2 as a path of least resistance measure because “killing you is hard.”
What about you, what is your favorite media villain?
Oh, it’s you. It’s been a looong time; how have you been? I’ve been really busy being DEAD. You know? After you murdered me? Look, we both said a lot of things you’re going to regret, but I think we can put our differences behind us. For science. You monster.
I find… we’ll just say “the villain” of Undertale compelling, but it’s one of my favorite games so I’m a little biased.
emm, actually, that’s from half life 2!