Ellie's parents were always busy with work so she was basically raised by her older brother, James, he didn't know how to raise a girl so he raised her like a boy. She didn't mind much, and didn't even realize he was until she was 12. Her brother was her best friend, he taught her everything he knew; everything he could and she loved him for that, and he was her hero. She looked up to him like a normal child would to there idol; he was hers.
She was 13 when she started to have unsettling thoughts, she had been raised to be a boy and this was weighing heavily on her now, she only knew how to be a boy. She was now scared about who she was, and she had no one to help her with these thoughts, she was so scared; She thought she was a freak, what kind of girl wanted to be a boy? So she ignored her feelings, ignored the ever lingering feeling that she wasn't who she felt like she was.
When she was 14 her brother got hit by a car, he died on impact and Ellie held him while he died. Blind with grief, and already skilled in alchemy (both her father and her brother taught her what they knew) she started to study human alchemy in secret and attempted to bring her brother back to life when she was 15, it resulted in her loosing her right arm.