Attack on titan (Shingeki no Kyojin)

After the fall of the government, the truth of the world in Attack on Titan is finally revealed: humanity still exists outside of the walls and they hate the Eldian race which the main characters are a part of. Eren's father Grisha turns out to be an Eldian from the country of Marley where he was part of the secret Eldian Restorationist group. In the society of Marley, Eldians are portrayed as the "enemy" of society, with most of them living within this country as second-class citizens forced into interment zones while wearing armbands. This is a clear parallel with the way Jewish people were treated during the Holocaust, though the story of the Eldians also has parallels with the histories of the Japanese people, North Koreans and many other other groups, so it's not written as an exact 1:1 metaphor.