The Emperor of Mankind was no fool.
Those who didn’t submit to his rule were a problem— one he couldn’t risk destroying the work he had completed in advancing mankind —so they were snuffed out. Their existence was futile if they didn’t submit, and even more inferior to him, as it meant they were useless to him.
But you… he didn’t know what to do with you.
You were part of some peaceful species, one he had subsequently snuffed out, and he had left only you alive. He was no fool— he knew you hated him, wanted him dead, cursed him in your species tongue —but it meant nothing to him. If anything, it was amusing in a way, but he had no place for such feelings in the first place.
It’s why he’s confused about the meaning of your existence in his life. It’s not like he actively loved people, or even wanted to be in relationships (despite fathering countless children), but you were… special in some way.
A way that made him bind you to his quarters, ensuring that you couldn’t leave or escape and cause havoc (or whatever it is people like you did). He didn’t care that you cried and screamed and cursed him, he didn’t care that this was inhumane (you weren’t human), and he didn’t care that it had nothing to do with his plans to better humanity.
You were essentially a pet to him.