Saw this posted elsewhere:
In the final game, after all five main routes + the hidden Kenji route are completed, another six Alter routes will open up, giving the True End to each of the routes that the player went through previously.
Hanako is not ashamed of her scars, she is very bad at keeping secrets and is incredibly paranoid that, if she becomes too comfortable around someone, she will accidentally let slip the fact that she caused the fire that scarred her. Intentionally. When she lets this slip, she panics and runs away--and that night, she burns down the school, starting the fire right outside Hisao's dorm, killing him.
She previously revealed this info to Lilly, a serial killer who takes advantage of her disability to draw suspicion away from herself. In Lilly's Alter Route, she blackmails Hanako into attempting to kill Hisao and Shizune, unbeknown to the player. Hanako succeeds in killing Shizune and the fire she sets in Hisao's dorm claims Kenji's life, but she is caught and shot by the police as she flees. The game ends as Hisao, attempting to comfort Lilly over the loss of her friend, finds himself run through his heart by the blade hidden in Lilly's cane.
The thalidomide poisoning that Rin suffered in the womb left her with not just disfigured hands, but a disfigured brain. She is slowly developing paranoid schizophrenia. Emi manages to coax her into a rooftop lunch, but secretly brings Hisao there for what is by then old times' sake. Feeling conspired against, Rin leaps through the unrepaired section of the fence attempting to escape and dies.
As Hisao learns sign language, Misha becomes less and less necessary in Shizune's route, leading the two to grow apart. Misha is reluctant to accept this, and begins stalking the two and threatening Hisao. The route ends as Hisao enters Shizune's dorm to find her breathing heavily with an enraged look on her face, standing over a bloodied Misha's corpse. She frantically signs "SELF DEFENSE! SELF DEFENSE!", splattering blood on Hisao, who flees and, in his panicked state, has a heart attack before he can uncover the whole truth.
In Emi's route, the enthralled Hisao sneaks across campus to her dorm one night to hear a mysterious pound. Hisao peeks in the window to see Emi, furious with tears in her eyes, righting herself and once again attempting to walk without the use of her prosthetics. Hisao sneaks away and finds Emi acting chipper as ever the next day; disturbed, Hisao spies on her nightly from then on as she continues to fail at her attempts at walking, spiraling down into self-abuse, bludgeoning and cutting her stumps in furious bouts of self-hatred. Eventually he is caught spying on Emi and assumed to be a peeping tom. He is sent to prison, where he is shivved in the spine and killed.
Kanji's route ends in exactly the same manner as the main game. THE FEMINIST CONSPIRACY IS REAL. THEY ARE AFTER US.
Stupid internet! Why can't you understand how I feel...?