[Kogami quietly listens to Danny's story. The pretext about his eye makes sense and to be forsaken by society because of that-- He knows how it feels yet he doesn't. To be forsaken by those who were supposed to love you because of a flaw that's not even their fault.

He can't even begin to think what that much feel like. The emotional trauma of a secret like that, he can't even begin to understand. He thinks that Sibyl would have intervened a long time ago if that were the case. Given Danny a fake eye that maybe he could see out of. Helped his mother. Sibyl, for as much as he hates it, could have saved them.

No words really come to him initially. However, it's not disgust and it's not judgement. It's actually Shinya Kogami thinking how to be a comfort in a situation like this. Usually he resorts to jokes and has a lack of tact, but that's not going to be useful here. ]

A mother should care for her child. It's not your fault she took her life. Unless there's more you're not telling me.

[His voice is gentle, but goading. His own mother still loves him despite the fact that... he had a fall from grace.]