I was searching around and reading a lot of theories... and I actually didn't find this one. (Which is shocking, though it might be out there and I missed it. lol)
Please, seriously. Read it all before you throw it out the window. Did anyone stop and think that the crazy dreams she's having is because she has done drugs??? This leaves room for other theories... in real life, rape, abuse, illness, transgender identity, etc are all reasons people come to drugs as a self-medicating behavior pattern. Hopelessness, depression, etc. Bear with me here:
Madotsuki is a young woman, late teens-early 20's, with a lot of horrible things in her past. Her parents died when she was fairly young (hence the zone full of disembodied armsand legs, and the two male/female heads that fly overway in that same area ONLY when she tucks into the cave and can't see them. Hiding from the pain.) This is why she lives alone. Then in highschool she was bullied.. hence, the Torinigen. Normal "popular" girls don't really do anything bad. Just ignore you... but some are vicious (the one with the purple eyes) and thats why they put you at a dead end. However, Madotsuki does make friends with Monoe. Thats why in the dream world, Monoe is normalish, not crazy scary. However, Madotsuki is overcome by greif when she watches Monoe die in a horrible car (or bike) crash. Monoe disappears when you try to talk to her, as a metaphor for her disappearing from Madotsukis life. Monoko IS Monoe... after the crash. So it makes sense that this would also haunt her dreams. Madotsuki has a pretty good reason to be depressed... and it gets worse. Poniko is the image of who Madotsuki wants to be. Hence, similar room. However, it is inescapeable to madotsuki will never be Poniko, so this idea of "Poniko" aka a perfect Madosuki turns into a monster/creature in her dream world. Being uboa, who leads her a horrible world. (the realization that she cant be this other person who she truely is not is depressing) this depressing state, where shes lost her parents, and her best friend, and feels like she'll never be the perfect person she wishes she could leads to what many depressed young girls turn to. (what they think is) love. Boys. Thats why the world uboa takes her to is filled with the white substance, and the background is a black monster devouring the pure white hills (symbolizing virginity). She's despirate for affection and to feel wanted.. but then she finds that teenage boys only seem to want one thing from her, she realises that their "love" is false, depressing her even more. When poor madotsuki is almost at her wits end, she finds someone who can actually give her true love and affection. Her music/piano teacher... Masada. The whole eye thing could mean that he had a real-life eye condition or something to that effect, but if he gave her real affection, why would that matter to her? Or, it could just be an effect the drugs add to her dream. Yes, I'm getting there. SO, she falls in love with Masada, and becomes pregnant. (Hence, her sleeping in his bed in the spaceship) This explains a lot of the fetus-shaped horrors in her dream world... but more on that in a minute. One day, however, Masada is killed in a train wreck. (trains/subways are a very common thing in Japan) This is shown after the space ship crashes, and you see what looks like a trainwreck near the fetus-like moster that crys (the one that when you stab it, the eye changes colors) Kyukyu-kun is a phallus shaped rainbow blob that you meet after passing through a zipper-like moster, which referances to the memory of the day when Madotsuki became pregnant. The room leads her to the FACE... an image of her horror at the memory of the abortion she had done, after the death of his/her father. A single young woman, so horrifically depressed, could not have raised the child. Now, the one thing good in her life, her only love, is now dead. Her baby is dead, because she knew she wouldnt have been unable to care for it, on top of the judgement she would have recieved from others. (judgement is a common fear throught her life, hence all the eyes and eye monsters in the dreams. "judgemental eyes") Her parents are dead and cannot be in her life. She watched her bestfriend die. Shes bullied at school. What is left for her? Like millions of real people in the world, she figures out that drugs can temporarily ease her pain, and help her feel better for short periods of time. She does not leave her room because she feels like there is nothing left in the outside world for her -it has all been stolen from her. When people become depressed, they often refuse to leave. When someone turns to drugs to self-medicate depression, they only want to stay inside and hide from the horrible world in their temporary relief. Drugs, and sleep. A conscious mind will be 'high' and temporarily happy on drugs, but dreams, which contain our subconscious fears and horrors, are often haunted when on drugs. They deform our worst memories and cause deranged, crazy nightmares. This is true in real life, a person on drugs is highly likely to have insane nightmares. Her whole dream world is induced by drugs that dig up the worst memories in her life. Hints of drugs are used also, aside from the pure design of the dream world itself, such as the creature in the mall known as "e-man" The character with an e for a head. E-head. get it? E is the common name for ecstasy, and in this room you can change some color options as well. This is a brilliant, sneaky refernce to the drug which makes you see colors brighter, and sometimes different. (also enhances hearing and visuals) Also, many minor characters and events can be explained by the influence of the drugs, that give it a "alice-in-wonderland" effect. Poor Madotsuki has lead this horrifying life, and when she wakes from her final dream on the drugs, she realizes that these drugs are only forcing her to relive the horrors of her life when she sleeps. With nothing at all left to turn to, she comes out to her balcony, and finally gives up. </3