Fall Cry 5 was a big one for me.
Spoiler: Major FC5 Spoiler
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When you realize the Cult was right, that the world was ending, and you just went on a spree to end their Doomsday Prepping.
It was a big blow to me, because of the fact that I realized that the 3 Children you killed were all in charge of some major operation that was supposed to help them survive their time underground.
The Child in charge of the drugs was supposed to keep the populace docile, since they were going to never see the light of day again.
The Child in charge of the military/culling was supposed to ensure the strongest survive. When everyone is in such a small space with limited resources, you'll need to thin the herd to make sure humanity can survive.
The Child in charge of propaganda was supposed to make sure that everyone works together and to avoid any kind of insurgencies. With such a small community and high tensions, everyone will need to work together to survive.
It was messed up, but they all had something designed to keep the human race going when everyone went underground. Then, at the end, it's just you, the cult leader, and pretty much nobody else down there. Because you killed them all.