As i see it Makoto has serious daddy issues. This could be the root cause of her depressions.
What she wanted/wants is affection/appreciation from certain people.
Mostly from her dad. -Not there.
From her mother. -She acts more like a friend or sister than a mother.
From Akira/Sensei as a dad replacement. -Not going to happen that way.
The moment she realises Akira wont/cant give her that particular affection/appreciation, she goes bluejay.
After (before due to reset) bluejay, her mother changes her behavior towards Makoto going into mom mode finally, which stabilises Makoto, getting the affection/appreciation she needs from at least one person she wants it from.
After she learns of her fathers supposed death she is depressed and might have tried to kill herself again.
Further reinforcing the idea that she has serious daddy issues.
Ami also really helped her grieve, and was there for her, after losing her dad. I think that's the main thing that Makoto needs. Someone to understand and be there for her, and like you said affection and appreciation.
Around Bluejay, all Makoto had was Miku, and Maki who love her yet don't really understand her, then there's Sensei who she thinks could understand her, but instead uses her. That on top of everyone else resenting her for everything she did for them, made her give in. After breaking then resetting, Makoto is reprogrammed to be scared of dying due to the dreams she is having of what happened and, so, tries another route with Sensei instead of jumping. She tries to get him to treat her more like a human being. I don't think anyone really helped her after Bluejay until after her dad died though.
Didn't she say as much and more during that creepy fuck in her room? Something like trying again and again but saying she thought she did at least which strongly implied getting reset back to life every time, i swear she mentioned almost the exact same thing after the bluejaying death reset sent her bonkers.
She implies she tried to kill herself but it always became a hallucination:
So, it kind of sounds like she committed suicide multiple times somehow without her mom noticing (possibly with pills that she's mentioned before), but it could just be her literally hallucinating due to sleep deprivation and having that "fucking dream" as she put it.