Most likely, he was still in middle or maybe high school when his parents died. He was most likely still a minor, since it's clearly stated that Mal took over the role of his mom and helped raise him, but his aunt would have likely become his legal guardian. Mal gave him a room and took over raising him, and she's clearly into the mommy roleplay. She also clearly has had feelings for him for some time, which is probably why she didn't tell him anything about Heather's departure or tell him to call her like she promised she would. It seems like she was intentionally driving a wedge between them so that she could get closer to him, herself.
I honestly don't understand why, after Heather's reveal, MC didn't immediately go off on Mal for what she did. Especially if on Mal's route, knowing she's been harboring feelings for him, he should have been furious, at least if on Heather's route. She took deliberate actions to break MC and Heather up and keep them apart for her own selfish reasons. I don't understand how MC didn't call her that night to chew her out.