How to get the Good Ending:
You must get as many murmering/flash points as you can as you venture throughout the game as every flash murmers gives you positive karma. They are obtained by listening to conversations, encountering certain dead bodies, or even miscellaneous things like squeezing a doll or playing the guaitar. And DESPITE POPULAR BELIEF, you can kill every single npc in the game and loot every bullets in every crevice you manage to find in metro stations filled with inhabitants, even chapter 3 "WAR" which starts with Frontline - Black stations. Once you recieved a certain amount of karma, easily done if you patiently listen to every conversation at the very least, you will automatically given the ending sequence to choose to save or exterminate the Dark ones.