Fallout: New Vegas...
*Boone's story...
*Veronica's story...
There are others in New Vegas but they're the most prominent.
*Boone's story...
Not only did he participate in the Bitter Springs massacre which killed hundreds of women and children but then later he was forced to mercy kill his preganant wife who had been enslaved and was tortured. He wanted to go save her but there were too amny Legionaries around and killing her was the only way he saw he could "save" her.
*Veronica's story...
Due to the Brotherhood's xenophobia they survive by pro-creating with each other, due tot his homosexuality is often looked down upon and for Veronica (who is gay) this meant she couldn't be with her love (who is heavily implied to be Christine from Dead Money). As she grew up Veronica was taught by Father Elijah who eventually became more and more crazy and obsessed that he abandoned Veronica and went about achieveing his own goals, lying to Veronica the whole time about what he was doing. Not only that but Veronica is also a very outgoing persona and if she travels with the Courier she sees what is happening out in the Mojave and wants to change the BoS. However, as shown in her personal quest no matter what she does and no whatever what proof you give, McNamara never changes his mind and for like the only time in the entire game Veronica actually puts all sarcasm aside and actually talks solemnly and with a very sad tone that there is no hope for the Brotherhood.
There are others in New Vegas but they're the most prominent.