The evil ending of Jade Empire immediately came to mind. Jade Empire was similar to KOTOR, only set in ancient China. Throughout the game your character is aided by some sort of benevolent spirit dragon that has been damaged by the baddies. At the end, you can either restore her strength or destroy her and take all the power for yourself. I played through that game several times and only did the evil ending once. It was like killing puppies evil. I pretty much grimaced and shook my head throughout the entire sequence.
I tend to play these games as I would if it was really me doing stuff. I'll gleefully kill pirates, thieves, evil corporate types and douchebags, and happily take their shit, but when it comes to storylines that require me to pillage and murder decent, normal, non-threatening folks, I don't enjoy it, and that's kind of the point of playing these things.
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