Hello!
Did you betray Kokoro? You monster! Just kidding haha sorry. The story does not change, only your relationship with Kokoro. Until you get her to forgive you, you won't be able to talk to her and your story mode dialogues with her will change. Also, even if you get her to forgive you, her romantic route is blocked, so you won't be able to do her personal quests.
I'm afraid Mia is not a character available for a romance. If you get 100 points from her on her exams for an entire month, you will unlock a sex scene with her. And, if you are not playing the easy mode, you can receive BDSM punishments with her if you are punished, also during the story mode there will be BDSM scenes with her, but that's all.