Origin (there are multiple):

She was a girl who lived during the time of World War II. She was playing hide and seek in her school one day and hid in the third stall of the girl's bathroom. However while she was crouched and waiting in the stall some planes came and bombed the area, causing that part of the school to collapse on her.

She was a victim of ongoing bullying by her classmates. One day the bullying got particularly bad and she ran into the third stall of the bathroom to try and get away. The other kids came and banged on the door to try to force her to come out, but she had locked the door and they eventually left. Later that evening some school staff members found Hanako-San dead in that same stall, she just couldn't take it anymore and had committed suicide right there.

Hanako-San fell out of the window of the school library. It implies that her fall was an accident, but doesn't give enough details for us to know for sure or even why she ended up in the third stall of the bathroom.

How to summon her:

all you have to do is stand very close to the door of the third stall, knock three times, and ask"Are you there Hanako-San?"

Afterwards there's always a stretch of silence which seems to last forever. Right around this time everybody else will tend to run out of the bathroom and abandon the poor person to their fate, alone. Then if Hanako-San is really there she will answer in a slow whisper "Yes, I am here."

According to the legend of Hanako-San what happens next will vary depending on what school you're in. Sometimes a hand will bust through the door and drag the person into the stall and kill them. Usually though after the pause the stall door will open just a slight bit. Then if the person is brave enough they will be able to push the door open, revealing Hanako-San herself.

Appearance:

Hanako-San is described as having very pale, white skin and as always wearing a red skirt. Her hair is short and black, done in an old fashioned style. It's obvious that she's a girl of school age, but it's not known why she will harm some people and not others. Sometimes she's said to even protect kids who are being bullied by classmates or are having problems with other ghosts.

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Well... Little girls are creepy!

Reference: http://anitasnotebook.com/2014/10/legend-of-hanako-san-spooky-japanese-ghost-of-the-school-bathroom.html