An item called the "Golden Dark Stone" appeared in Explorers of the Hero's Ruin!, where it was hidden in the Hero's Ruin. It was sought by Cedric Juniper. Unlike the Dark Stone, this item was golden instead of black, and merely summons Zekrom instead of being its dormant form.
In the manga
The Dark Stone in Pokémon Adventures
In the Pokémon Adventures manga
The Light Stone and Dark Stone initially resided at the Desert Resort, where they were found and excavated by Clay and his mining team in Lights, Camera...Action!. After investigating the stones, he felt worried and called Lenora to come and investigate them with her expertise on ancient artifacts. Lenora took both stones to her museum, but only made the Dark Stone discovery public so that the Light Stone could be kept a secret. Later, Lenora called Drayden to help her investigate the stones, which helped them realize that they were actually Zekrom and Reshiram.