This War of Mine kind of messed me up. One place you visit, there is an armed soldier who is about to rape a girl. Of course, I tried to take him out. His weapon was way, way better than mine, however, and he killed the character I was using to scavenge. This was devastating to the rest of my survivors and ultimately spelled the end--depression set in, a couple wandered away, and the last one hung himself. It was a "Game Over" that left me stunned.
The next play-through, when I returned to that place ... I let him take the girl into the back room and then looted the place while the soldier was occupied. I hated that, as did the rest of my team, but it was the only viable option. That was an unsettling slice of "real" in a video-game.
In Fallout 4, I really struggle with siding against the Brotherhood. Not because it's the Brotherhood, I hate what they stand for, but because it means I have to kill Scribe Haylen. She's a good person and a sweet girl who really cares about her comrades. If you join them before deciding to fight them, it feels like you have to kill a friend. More than that, it makes you realize that a LOT of the regular soldiers you're killing are probably good people, as well.
In Skyrim, when that one group wanted me to kill the Dragon that had helped us. Jeez, I did not want to do that. Like, at all. But, I did it, because it seemed like the smartest way forward. I felt so crappy afterwards, though, and looking down at the Dragon's dead body, I though, "my character would not do this." So, I reloaded, and kept him alive. Next time I played, I used a mod that let me have my cake and dragon, too.
In Divinity: Original Sin 2, there is an encounter where someone on your side (X) captures a former friend and comrade (Y). They used to be in the same Order before the person on your side decided to leave. You have the choice of trying to convince X to be merciful or allowing them to execute Y. I convinced X to be merciful. Later, you find X burying his parents. It turns out that Y killed them after you let him live. Ouch.
