At the beginning, the only known information regarding Misao is that she had mysteriously vanished three months before the game, with many of her classmates believing that Misao was already dead. In addition to that, a conversation overheard by the player from other classmates (Tohma, Yoshino, Saotome, and Kudoh) reveals that she may have had a crush on Tohma and was bullied by Yoshino before her disappearance. After, several strange paranormal events began and it's discussed amongst the others that these may have been Misao's doing. When Tohma jokingly and mockingly asks Misao to 'spare' him from her wrath, Misao unleashes a true curse and sends the school, and everyone in it, spiraling into an otherworldly realm filled with terrifying monsters and ghosts.
Misao originally contacts the player through their dreams and minds, asking them to "help" and "find her". When she enacts the curse, the player is the only one who can still hear her voice, continually pressing the character to find her.
At the end of the game, Misao reveals to the player what exactly happened to her before her disappearance in a series of flashbacks. First, she shows the event where Yoshino told everyone in the class that Misao had a crush on Tohma. Shocked and embarrassed, she withstood the teasing until Tohma came up to her and responded that he had a crush on her as well, reciprocating her feelings in a surprising turn of events. Yoshino stood by and incredulously commented on the affair until Tohma told her to butt out.
The next flashback showed Misao wondering why Yoshino would blurt out her hidden crush, but brushes it off in a kind manner and decides to thank the pink-haired girl instead. She then receives an embarrassed text from Tohma, telling her that he liked her and asked if she liked him back. The scene cuts off as she writes her reply.
Misao then shows what happened afterwards, in which the text is then printed out and tacked onto a bulletin board for everyone to see. In the background, we see a character sprite of a long, blonde-haired girl that may or may not be Saotome, turning away from the bulletin board when Misao runs up to it before walking away. The text itself was filled with Misao's private feelings towards Tohma, including the poem she'd written, and she runs away in dismay.
In the following flashback, Misao slowly walks back to her classroom, theorizing that it was Yoshino who had took a peek at Tohma's phone then published the text. She also correctly guesses that Yoshino herself liked Tohma, but defends her position as Tohma's girlfriend solidly before she's about to head back into the classroom. Unfortunately, Misao instead overhears Tohma talking to Saotome, saying that she was the only one who he had shown the same text to and pressing her for the truth. It's a little vague if Tohma was fooling around with Saotome or if he was actually just confronting her, but from the outside of the classroom, it sounded more like the former. Most likely feeling betrayed, Misao runs off yet again, but this time a sympathetic Kudoh is seen watching her leave.
In an abrupt change of pace, the next scene depicts Misao being bullied in a bathroom by Yoshino and two other girls. She doesn't fight back, but she does remark that Tohma will never make Yoshino his girlfriend if she continued to bully Misao. This caused Yoshino to become even more violent, finally taking part in actually hitting the poor girl. Determined to make Misao regret her words, Yoshino takes a nude photo of her and blackmails her into silence for all the bullying that she's endured up till now. Then, she encourages a boy to "give her lots of love", locking Misao in the bathroom stall to be raped by him.
The next flashback shows Misao sobbing in the bathroom stall, most likely having been left there after the boy had raped her, and night had already fallen in the school. She hears a voice and it is revealed to be Mr. Sohta, who had probably heard her crying, and chastises her for being out so late. Unable to stay calm, Misao breaks down in front of Mr. Sohta and he comes to her side as the flashback turns black.
When we next see Misao, she's seen sitting at Mr. Sohta's desk, with Mr. Sohta comforting her and asking her what was wrong. This directly contradicts a statement the teacher had made to Aki before, in which he had said he didn't have time to listen to Misao and had ignored her. Watching the events unfold in the background, the player then learns that the bullied girl lied to Mr. Sohta about the physical and sexual abuse, probably in remembrance of Yoshino's blackmail. Misao instead tells him that she'd had her heart broken and that she was crying to herself in the corner of the bathroom. The older man replies that he himself had been like that once, but Misao had found that hard to believe, complimenting on his gentle and popular nature. After comparing his own past to her, but remarking that she was much more 'charming', Mr. Sohta then hugs her from behind, causing her to become confused and uncomfortable.
He then reveals that the rumor of his hand fetish is true by admiring Misao's hands, and she pushes him away in fright. She backs herself into a corner, but Mr. Sohta continues to pursue her as the scene fades. It is assumed that she is raped again, this time by Mr. Sohta. Off screen, Misao screams and the teacher yells back, outraged at Misao's rejection. When the screen comes back, Misao is dead, with Mr. Sohta standing over her body.
Mr. Sohta then drags Misao's body to the same bathroom stall where she was raped the first time and holds up a saw, dismembering her body.
Three months later, Misao invoked a curse upon the school that was only reversed when the player found her head, heart, eyes, arms, legs, and brain, then chose the final sacrifice, the curse filled the school with monsters and traps that often prove fatal on encounter with few exceptions, some traps scary (like the "you're dead" paper) some relatively bland (hitting head on wall as phone rings), only Tohma, Sohta, Onigawara, Library and the player survive long enough for the collection of Misao's parts however, ether Sohta or Tohma must be killed to end the curse, freeing Misao's soul.
During the "True Ending", Misao returns to torture the souls of those who died as sacrifices, namely Kudoh, Saotome, Yoshino and either Tohma or Sohta, depending on who the player chose as the last sacrifice earlier. In all of the player's attempts to bring the sacrifice back to life as reincarnated babies, Misao is a constant presence and is seen tormenting them all.
When Aki tries to rescue Kudoh, he is in a dark, empty room with clones of Misao surrounding him, all of them telling him things along the lines to die and suffer. When the player manages to convince Kudoh that the Misao surrounding him was only an illusion from the darkness in his heart, the Misao clones disappear. The real Misao then appears, saying that she didn't hate Kudoh and that she was happy he thought of her.
When saving Saotome, the cutscene continues with Misao appearing while Saotome and Tohma are having lunch together. Upon seeing Misao, Tohma goes to her, acting hypnotized, and proclaims that he was only playing around and lying to Saotome and loved only Misao. Anguished by this, Saotome will take the bat from the player and attack both Misao and Tohma.
When saving Yoshino, Aki finds Yoshino in the girl's bathroom, wearing only her underwear while being beat and bullied by three Misao clones. The clones are stopped when the player beats them each with a bat. After Aki talks to Yoshino, Misao then appears her face covered in shadows, and she angrily questions the player's motives for interfering. Aki says that vengeance would not help her soul from moving on and Misao tells her to shut up many times before fading away.
Depending on whether you chose to sacrifice Tohma, his cutscene varies. If Sohta is sacrificed instead, the player would find Misao and Tohma after saving the three other sacrifices when moving on. Misao tries to coax Tohma to stay with her in the dark realm but Tohma is terrified of her, screaming monster as he tries to run away from her. Misao ponders on this, and Aki reveals that her desire for revenge has changed her, and gives Misao the little hand mirror.
When Misao looks into the mirror, it reveals that her vengeance has made her grosteque, making her eyes white with blood dripping down from them to her chest. Horrified at her new appearance, Misao turns and runs away from Aki whilst screaming not to look at her. Aki then consoles her, and Misao's spirit is freed, turning her back to normal.
Aki then is returned to the classroom, wondering if it was all a dream. Looking at the chalkboard however, she sees a message from Misao. She then says "No, it wasn't a dream... I'll never forget you... Misao." And the message on the board read "Thank You".
It is unknown if the police/law enforcement investigated Misao's disappearance, however, unless Aki was questioned, the case was most likely thrown out since Sohta, the murderer, was already dead, so there would've been no one to imprison or put on trial.
