Ok, how I like to think about Chara:

Originally, when she was alive, she was mischievous. That's what caused her to get sick. And before she died, she faintly saw what happened to Asriel.

So, when she came back in the genocide run, her soul was stuck with Flowey in the underground, however she could not be noticed by anyone, because it was only half there.

So, when Frisk fell down, she took her chance to maybe have another chance at life and see her family again. However, because of the mixed emotions in her soul, she went on a rampage, and killed monsters as Frisk, and was blinded by anger of her own kind. She mistook the monsters as humans in her vision. Soon, when she saw that she had killed Toriel, her "Mom" she became enraged at herself and wanted to stop. However she could not. Her soul had already been stained and Frisk was no longer there with the souls. Chara was only faintly there. What took up the rest of her soul?

You know when you become extremely sad, or angry, and you have a headache...

There's that clump of pain in your head?