Relatives Everywhere
Metal-tan, also known as machine girl, could be the lost older sister of Smile and Hou (Smile's little sister), this can be proved by the fact that she has the same cross like tattoos on her eyes just like Smile. Doctor-san aka Doctor Ochki and Nurse probably can be parents of Smile and Hou, who made it all possible to not let their children get infected by sickness "Rust". The Girl in a yellow dress, aka Sato, is possibly the older sister of Oreko. This theory has some proofs, the color of Sato's dress and hair are almost like Oreko's, since in the hospital Sabi can find the child version of Oreko, who is brown-haired, meaning it's her true color of hair and Sato have a slightly dark but still brown hair, but even the dress of Sato has the same color's shade like Oreko's clothes. Before disappearing of Sato, Sabi gave her a promise that she cares about Sato's Lil sis Oreko, more or less Sabi cared about Oreko. Also, it seems that Sato can be older than Sabi by approximately three or more years. And final of theory, Gas Mask Maid aka Cleaner, in truth can be the Mother of Sabitsuki, probably since Sabi had a sickness her mother had to work on many jobs, like bartender, cleaner and maid of course, and since Sabi's sickness seems too contagious, Sabi's mother always wears a gas mask when visiting her daughter, that's why Sabi remembers her like that. About true end, Mother as Cleaner understands that Sabi is not her daughter but Rust, a danger to every one person, knowing that only what Cleaner can do is end Rust's life and probably bury her dead daughter, but at least in other world, free from her sickness and evil side to make her happy.
Theory 1/example
Based on how Sabitsuki never leaves her room unless she accesses her computer, she may be known as a shut-in. Some of the NPCs she encounters maybe some of the only friends she can have or access. Hating reality, she goes onto her computer and tries to escape responsibilities in her life. In the School, she gets chased by the Red Demons, or Kaibutsus, at a certain point. This could mean she was bullied or even harassed. While you see countless demons trying to get her while she is running through the hallway, this could mean she is a target in her school. Knowing how Smile never seems to be a nuisance by trying to kill her in any way, could be a friend to her as well as some of the other NPCs. However, you see Smile the most around the dream world, possibly for support. Another example is how she can get possible revenge on a certain NPC Kaibutsu, where she tries to stand up to it when you select the Pipe effect. When you try to hit it, it automatically turns around and kills Sabi.
Another theory I have come up with is that .flow takes place in an apocalyptic world. Seeing how it is always a darkish grey-green sky when you go up on the balcony. The Human Brain is also not creative enough to imagine another living human being. Possibly based on how Sabitsuki can go outside on her balcony that is the only possible way for her to see any other human. As for Smile and Hou, they could be neighbors or someone who she just happened to see all the time, possibly a close friend maybe.
Sabitsuki Beat Her Classmates Up Mercilessly
Sabitsuki was getting bullied so badly that she took a weapon to school (Maybe the metal pipe she uses in this case) and she beats some kids up for tormenting her, causing her to be sent to a mental hospital of some kind.
The hospital themes in the game may represent that situation, like the kids she beat mercilessly.
Sabitsuki is Diseased with "Rust"
The most telling sign for this theory is that Sabitsuki's name means "covered in rust".
Sabitsuki may or may not be able to leave her room due to being quarantined. The disease, known as "rust", has visual signs of infection - namely, the rusty colored skin/potentially blood discoloring many characters skin. There are lots of dead and dying children in the corrupted Children's Hospital, these children (especially due to Little Sabitsuki in her bed there) could very well have also suffered from rust disease. Part of the disease could also be present in the Erosion Counter - certain traumatizing events cause Sabitsuki to be forced out of .flow and into the real world, with blood splatters (and later, weird machine-like things hooked to her monitor) appearing in her room. This could be a start to her body succumbing to the rust.
Red Demons are The Disease Attacking Sabitsuki
There are almost no demons when playing as Sabitsuki, the only ones appearing in the Flesh Walls world, which is heavily theorized to represent Sabitsuki's body. If this is assumed to be true, the demons in the Flesh Walls world could represent the rust starting its take over. Once dropping the effects into the PC, a small clip shows a small Sabitsuki being birthed in a mass of viscera. This could represent the rust's full takeover of Sabitsuki, hence the reason Sabitsuki from then on is referred to as Rust, and her color slightly changes to a more sickly tint. Ending 3, also known as the True Ending, shows Rust walking through long halls that highly resemble the Children's Hospital. Each hall gets more and more deteriorated as more demons start attacking her. Rust reaches another version of herself (or Sabitsuki) in a throne and kills her. This could signify Rust taking over and finally killing Sabitsuki, or Sabitsuki killing the rust disease inside of her, depending upon your interpretation.
The Maid in The Endings is Fairly Innocent
The other two endings, instead of revealing less of the final true ending, actually show exactly what happened. The first ending is due to Rust not having control of Sabitsuki - she finally leaves her room. In the second ending, Rust begins taking over Sabitsuki's body but hasn't fully killed her yet (gone through the corridor). The Sugar Maid comes in to take Sabitsuki away to take care of her, and Sabitsuki ends up dying in her arms. The third ending, Rust has fully taken over Sabitsuki's body and the Sugar Maid comes in and kills her to rid her of the disease once and for all (or possibly in self-defense, as Rust comes closer to her with a grin on her face).
The Black-Haired Girls are Sabitsuki's Immune System
The girls who heavily appear in the Flesh Walls world could easily represent Sabitsuki's immune system. The ones outside of the Flesh Walls area appear to be sick or dead - the one in the Hospital is in a bed and the one in the white room is with the dead children. To get to the Dying Girls event, you may have to kill them off to see the scene (however, this can be avoided with the use of the whistle effect). Going near any of the girls as Rust will automatically kill them. When getting the hospital GET as Rust, once entering the room preceding the Dying Girls event, every black haired girl in the room dies. This could symbolize Rust and her disease brutalizing Sabitsuki's body and her immune system.
Flower Genocide of Hana
Flower Girl aka Hana, seems to have once been a biologist and made research on plants, but with her curiosity in plant world made her go too far. In fact, she created some possessing plants and these plants can control anyone who they entangled. In the end, these plants made Hana their queen for the price of her freedom and she can't leave this plant maze that she made, so she created her flower genocide. Anyone who entered in this plant maze became slave of plants forever, except Sabi, who somehow probably with help of her second personality Rust can save herself from this cruel fate.
Oreko caused the Rust Infection
Despite her young age, Oreko is genius. She seems to mostly research the deep sea but in the same time she is an inventor, and in her underwater house Sabi can find a very large and strange machine, and sometimes Oreko can be seen sitting near this machine and trying to fix it, probably knowing that Sabi is sick. Oreko tried help to her by creating this machine but in the end, the machine didn‘t work, and instead of curing it, it spread the Rust Infection all over the world, how not strange not everyone got this infection, and it's proving that Oreko is the accidental culprit of the Rust Infection.
Sabitsuki Had a Deficient Immune System
Sabitsuki was born with a deficient immune system (possibly HIV+) and had to be installed with cybernetic organs as a result of disease soon after birth (hence the "machine" effect). She was born around the time of the first outbreak of the Rust illness, which killed many children at the hospital she was in. However, she survived due to her isolation (as seen with Little Sabitsuki in the Parade ward, located in her separate room before the erosion meter increases). When she uses the computer, she uses an experimental form of virtual reality intended to be used for psychological therapy based on her thought patterns, made possible by the fact she is a cyborg. Even though she had been previously employed as a beta tester for this technology before she contracted the "Rust" illness (which she was more susceptible to due to her weak immune system), after her diagnosis her mental world rapidly changed as the knowledge of her illness mentally consumed her. She continued to test the system as her wages rose due to the special insight gained from her case and to incentivize her to continue testing in spite of the mental stress, but being placed under quarantine, she was unable to do much with it.
Oreko was a childhood friend who she met as a result of her being the daughter of a scientist her parents met specializing in cybernetic enhancements. She grew up around her father's machines, hence why she is often seen with them.
Sabitsuki becoming Rust represents her entering the terminal stage of her illness, with the ending depicting a maid/nurse, assigned to her apartment block to care for her wearing a mask (as presumably the disease is airborne - the same way that oxygen rusts metals), before "euthanizing" her with a chainsaw (possibly meaning the disease cannot be stopped by bullets). The rust corridor represents the disease killing Sabitsuki off, with the smile that appears when she encounters the nurse being the disease beginning to physically manifest itself.
Sabitsuki is Depressed
Sabitsuki may have depression, and might be hurting herself with some type of VR system, or may have some kind of disability/disabilities that make her do so.