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.
In Archie Sonic the Hedgehog Comics, a black Chaos Emerald serves as a holding chamber for Chaos and Tikal. The Ancient Onyx also looks a lot like a Chaos Emerald, but Sonic stated that it wasn't. There was also a black Emerald in the British Sonic the Comic. It was shaped like a Chaos Emerald and was located in the Shadow Dimension until it was destroyed by Sonic.
Black Coloured Chaos Emeralds in Fanfics
Black Chaos Emerald in user:Mystic Monkey fiction
The Chaos Emeralds' backstory are shrouded in mystery, and they are known to have existed for milleniums, along with the larger Master Emerald. However an eighth Chaos Emerald was "artificially" created in the future. Despite this, this very emerald has been prophacized since Echidnan times and there has been some accounts of it throughout history.
Eggman Nega, a genius, yet evil alchemist, created his own eighth Chaos Emerald that consist purely of negative Chaos Energy. Doing so had a serious effect on Mystic disabling his potential with Chaos Energy, unable to use the Chaos Emerald for even standard abilities.
This emerald also is also a major plot device in Ultimate Sonic.
Black Emeralds in Draconai's Fanfics
In fanfiction by Draconai, the Black Emeralds are a separate set of powerful gems similar to the Chaos Emeralds; they are even used by Zyx the Hedgehog to achieve one of six Super Forms. The difference between the Black Emeralds and the Chaos Emeralds are that the Black Emeralds are composed purely of dark energy, rather than the positive and negative energies which reside in the Chaos Emeralds. As such, the only ones who can utilize the Black Emeralds are those who are attributed to darkness, such as Zyx and the Nightmakers.
The Newmoon Emerald
As the Black Emeralds are dark counterparts to the Chaos Emeralds, it would make sense that they have a unifier; the Newmoon Emerald acts as a Black counterpart to the Master Emerald. Unlike the Master Emerald, which is needed in conjunction with the Chaos Emeralds to achieve a Super Form (save for Mecha Sonic), the Newmoon Emerald can be utilized solo to achieve the second level of Super Form of those who are able to utilize their power. It is also used by Zyx in conjunction with the Black Emeralds to achieve his ultimate form.
For more information about the transformations of Zyx the Hedgehog, see here.
The Black Emerald in SRB2
In the popular Sonic Fangame, Sonic Robo Blast 2, the Black Emerald was only to be obtained when the played collected all seven Chaos Emeralds, beat the story mode, and go back to Green Flower Zone Act 2 where the player than had to look for Red XII to obtain the emerald so the player can trun into Hyper Sonic.
However, you can only get the Black Emerald in version 1.09.4; anything higher will not have this emerald.
Main Article: Dark Emerald