It's a bit similar to the plot of Avengers: Infinity War where Thanos wipes out populations with the intent to "save them."
The story starts out with the major cities of the Earth disappearing one at time (along with their populations), starting with the most populous, in descending order. After all the large cities are gone, people start forming in ad hoc refugee camps.
The story centers in on a lady who had been travelling between cities when they disappeared, and lost all of her family members who were back at her home. At some point, human-like, but very alien aliens start making their way through the crowds, sometimes helping the sick and wounded, but mostly observing, and/or doing things the humans don't understand.
At some point the lady corners one of these (seeming) aliens and asks what is actually happening. The alien tells her that the aliens did not want to see the humans kill themselves or live out sick miserable lives, and after it became apparent the humans couldn't stop any of the bad things from happening, the decision was made for the aliens to step in and protect them.
So the aliens reduced the population (the first time you know for sure that the missing cities were destroyed), and they will leave a permanent team of wardens on the Earth to make sure humans don't mess up too badly.
The lady, heartbroken and shattered by the loss of her family, tells the alien that humans will hate them forever and never forgive them. The alien calmly tells her that maybe the people alive now will hate them, but most of their children won't, and even more of their children's children won't, and that in just a few generations people will love the aliens for the great kindness they have provided. The alien said this with a great sort of slightly mournful omniscience, as if, had the lady been much, much more advanced, she would see things as clearly as the alien did.