I had forgotten that I took notes as I was playing the game. I shoved them off in a corner of my Dropbox and forgot about them, but they contained the answer to this question.
In both the Mizuki and Nekoko stories, Aeka attempts to commit suicide by jumping off the roof. She survives, but is hospitalized. She leaves behind a note accusing her tormentor, Kyouka Nanjou, which seems to lead to Nanjou's expulsion.
In the Mizuki story, after Mizuki leaves school, Kouhei becomes the student council president. Because of what he saw happening to Aeka while they were classmates, he makes bullying his signature issue and tries to end the culture of silence where bystanders protect the bullies for fear of being targeted.
As far as I can tell from my notes, the Nekoko story says nothing further about Aeka's fate.
In the bad ending, where you don't complete anyone's story, the narration states that Aeka just disappeared all of a sudden from school. Interestingly, you can get this bad ending even after Aeka has already attempted suicide and jumped off the roof. So she attempted suicide, was hospitalized, and then just disappeared all of a sudden from school.
