This is a conclusion I've drawn after hearing the first 5 songs various times... It's really disturbing.
(It is recommended that if you don't know the lyrics well, read them while you read this)
So, this is the story of a girl who suffers from a series of misfortunes through the 5 song set, let me explain.
The Glass Prison: Firstly, we learn about this girl, who is clearly an alcoholic (or maybe addicted to smth else?) who struggles with this and realises that it has to stop, so she gets into the AA program, which is fairly religious btw. She was apparently dating someone but the person left her because of her addictions, thus, she decides to get rid of this. After a strong struggle in her mind (represented by the instrumental section), she grows convinced that God is the only one who can stop this, and leaves her faith in his hands.
Blind Faith: Months pass by, but she is unable to leave her addictions, she continues to consume alcohol even though she had promised not to. Begs to God to stop it, but it doesn't work. She begins to wonder on whether or not God actually cares about her, and begins to lose her faith. The entire song deals with her making up her mind and deciding that it is just not worth it.
"Hear me, speaking, asking why I even bother"
"I've painted my own Mona Lisa, she's fixed everything, Now I'm spoiled beyond my wildest dreams"
"Take the streets, the beaten path"
The instrumental section represents her final duel with God and eventually severing all ties with him.
Misunderstood: Having convinced herself that God can't save her, she leaves the AA and starts to think backwards (represented by the reversed JP solo) of her life. She realizes that her life is meaningless, and that even though she has been surrounded by people, it has been useless: Not only has God been unable to save her, but the people around her do no good either. She sees that she was Once happy, but now she's just a shadow of her being and sets herself deeper into her addiction. Goes bankrupt, becoming a beggar. She loses control of herself, submerged in delusion and had also lost her love, pure disdain for herself.
Upon seeing the misery of life she has, she decides to end her life through unspecified means, which she carries at her home. The last mess strange 3 minutes of the song deal with this. With whathever she has done to end her existence affecting her brain and thoughts, making a lot of random noise, which also represents utter desesperation. In the end, everything falls silent.
The Great Debate: Her ex-boyfriend, who loved her dearly but couldn't be with her because she just made him suffer because of how much much he loved her, learns about this. Unfortunately, her suicide failed, and she's left in a paralyzed state where she's conscious, but unable to do basically anything and several senses lost.
He gets into the stem cell experimentation, desperately seeking a way to heal her and return her to awareness. Learns about all it does (since he's a medicine student) and what it takes, and takes testimonies from other people. A medic especialized in this offers him something that MIGHT be able to save her, but it involves ending innocent newborn lives, so he has to deal with this.
He debates in his mind whether or not this is the right thing to do, and puts the good and the bad things to see what he's going to do.
Disappear: In the end, however, his morale wins, and he decides that he cannot sacrifice other people's lives for his own desire. Since she had basically no close family members left, he signs and agrees to euthanize her. Accepting her end and being in total misery, suffering because he remembers the good times she had with her, but regretting forever for not being with her. In the end, he realizes that she'd want him to move on, and he does.