The core thesis of Halo is "if soldiers were allowed to do whatever they want, they'd destroy the world". Halo 1, Chief wants to fire the ring and Cortana stops him. Halo 2, Arby wants to genocide the humans and everyone says that's a bad idea and then he gets genocided. Halo 3, Hood wants to do a heroic last stand on earth and everyone says that's a bad idea. Halo ODST, stop killing huragok they're slaves. Halo Reach, stop going down in a blaze of glory and carry cortana. Halo 4, stop putting your giant phallic ship before earth. Also the whole reason for the human covenant war is that Truth lied and started a genocide to avoid admitting that humans are gods.
Every single game is about soldiers and politicians making bad decisions based on violence, hate, and pride until a scientist or a smart person stops them and explains what's actually going on.
The Master Chief has massive psychological trauma from being a child soldier. That trauma has always been a central part of his arc, and whether the covenant's invasion justifies Halsey's actions in retrospect has always been a central question of the universe. The reason Halsey is kind of a Nazi is that she's implanted with a Geas by the librarian to follow in the footsteps of the Forerunners, and the forerunners sucked. Halo is concerned with big philosophical questions, and I like those questions, and none of the answers to those questions say fascism is okay.