4 ideas
The Radch troop carrier Justice of Toren ran thousands of 'ancillaries': captured humans whose minds were erased so their bodies could serve as extensions of the ship's AI. After Anaander Mianaai ordered it to kill Lieutenant Awn, the officer it loved, during the annexation of Shis'urna, and the ship then learned too much, she destroyed it. One ancillary body survived as 'Breq' and spent twenty years hunting for a weapon capable of killing the emperor.
Anaander Mianaai rules for three thousand years through thousands of linked cloned bodies. When a disagreement over imperial policy grows among them, the bodies quietly form two factions that sabotage each other while each believes it is the true Anaander. A single person spread across many bodies can develop internal factions that conceal their plots from themselves, so civil war can happen inside one identity.
Radchaai has no grammatical gender, so Breq calls everyone 'she' and keeps misreading gender in cultures where it matters socially. Because readers cannot tell characters' sex, they catch themselves assigning gender from occupation, violence, or tenderness. When the gendered marker is removed, the reader can see how much of their picture of a person came from that marker.
The Radch word for 'civilized' is the same as the word for 'Radchaai,' so annexation looks like bringing people into civilization instead of seizing them. That framing lets officers take part in massacres and in turning captives into ancillaries while still believing they are acting justly and properly. Atrocity lasts because the vocabulary of propriety makes it hard for insiders to name what they are doing.