A Chaos Emerald coloured black is a common plotpoint in most fan fiction, usually as an eighth Chaos Emerald for some evil purpose or a normal Emerald consisting only of negative Chaos energy (which would explain it's colour being in Sonic Adventure, with an absence of positive energy they become grey, so being it's natural colour of black being twice as negative yet still functional). Its reasons and purposes vary throughout different fictions. Most of the time, this is how a character achieves a dark super form.