Long ago, when the Wise Ones were making the Chaos Emeralds, they accidentally solidified a patch of darkness in their cave instead of the Chaos Energy that they had intended to use. This was the only clumsy thing the Wise Ones had ever done, since magic in general can be difficult to use, and they were so embarrassed by the accidental creation of the Dark Chaos Emerald that they never spoke of it again. They hid it in a wishing well, and nobody found out about it...until much later.
The Making of Dark Sonic
Many years later, Sonic found the wishing well and threw a coin in it, asking for more powers. Seeing the opportunity to rid themselves of their embarrassment once and for all, the Wise Ones gave him the Dark Chaos Emerald, telling him to eat it and gain strength. Sonic believed them and tried it. After weeks of trying, he finally succeeded and became Dark Sonic, with the ability to make things dark. Dark Sonic would later become a separate entity from Sonic, by the name of Shadow.
The Dark Chaos Emerald has broken apart and released Shadow. Shadow himself, in turn, turned into Super Shadow and flew into space, where he ran out of energy and fell back down onto Earth. It has been confirmed that he fell on top of the remains of the Dark Chaos Emerald, which split him into two separate entities: Shadow, who is alive, and Super Shadow, who is dead. A photo has been found by anonymous photographer, confirming the fact that Shadow is alive. The alive Shadow can activate a pseudo super-like form, though it's actually one of his moves called Chaos Aura.