I agree with those who said to go today, immediately, to the superintendent. But first I'd tell the principal, in person , that you are going over his head to his boss and the school board today, this day, and you cannot let another 24 hours pass with your niece experiencing daily trauma. And I'd get the counselor on notice that there is serious trouble.
Also, is your niece in counseling (outside school) for what has been a difficult few years? I'd get her some right away but emphasize that it is NOT because SHE did anything wrong or bad. Your niece is potentially very fragile, having lost her parents and having to deal with a permanent physical issue, and this bullying is the kind that could push her into a serious depression or worse. She should not have to transfer schools because as another person noted, that upsets her support system and SHE is not the aggressor.
And be ready for the board/superintendent to kick your complaints right back to the school and principal. At that point I'd be clear that your next call will be to someone outside the system that the school won't want to hear from -- police, or an attorney. And follow up on that threat if you need to. Police may be reluctant to get involved unless there is physical aggression, but it can't hurt to see if they will come to the school for even a general talk about bullying, at your invitation.
It's tempting to call in the media but that puts your niece's story out there for the world, and may end up getting her bullied or teased by other kids, and she may not want to be identified for the entire community as "the orphan girl who lost a foot and got bullied." She's at a sensitive age and won't want the attention.
For any interactions you have with the teachers (who probably want this bully gone as much as you do but are sadly given no power to do anything real about her!), the principal, the board or superintendent or counselor, document everything, keep every e-mail (make paper copies too), make notes about every phone call and meeting. You may need it later.
The way a class bully was handled by my child's teacher was that the bully was seated at a desk that was actually practically attached to the teacher's desk, it was so close. The child did not sit in "blocks" with other kids. He spent much of each school day doing his classwork INSIDE the principal's office, not in the classroom, and he was watched like a hawk if he was permitted the privilege of recess with the rest of his class. But this was in first grade, not fifth, where the teachers are under so much more pressure. This worked for this kid, but a seasoned bully like a 12-year-old may blame your niece if she (the bully) is isolated like that, and could try to get to your niece and bully her worse. I wish I could offer more ideas. But the thought of your dear niece with one more day of this is horrible.
Yes, as others said, call all the parents of your niece's good friends and alert them and ask them to ensure their kids are supportive and don't follow this bully's lead. And set up play dates frequently with your niece's friends so she can be distracted and have fun.
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