Like, say there's a quest to kill a certain character(s).
The thing is, you like those characters, or you think it would be wrong to kill them.
But you have to do it in order to complete the quest.
Have you ever come across a situation like this in a game?
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In KotOR when you have to kill all of your light side companions on Rakata Prime, dark side playthoughs of that game are difficult to morally complete. Slaying Mission, Jolee and Carth, especially Carth, was pretty difficult to do.