Just me running a darker version of the timeline besides some other changes I've made.
Also I can very much see the Elders doing that as a way of population control and making sure the humans don't try to rebel anytime soon, even if it costs them some genetic material. Also helped them wipe out several major cultural influences for earth so they can push their own culture on earth.
Sometimes they do go, we should have destroyed less of the populace, but still felt it was necessary with everything they're having to do to keep the planet under their control, work on the Avatar Project, keep their alien slaves under control, and other things. It's all very taxing though they don't want anyone to know that.
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To also answer another question I got ages ago, but tumblr ate it, I like to run that even though the Elders frequently have ADVENT culling the populace not in the Cities or approved settlements, they gather the bodies to be processed so nothing is "wasted." Working that into my fics. Why it's dangerous for XCOM to even try and go back for any fallen comrades if a Haven Retaliation goes south or if the area has "cooled" down and want to help people gather their dead, there still may be some ADVENT activity with gathering the bodies. And if there's no more ADVENT, there's barely to no bodies left.
One of the few instances of them not being too wasteful.