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.
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.
The Dark Stone was sought out by Team Plasma, who, led by the Shadow Triad, attacked the Nacrene Gym in The Battle Within in order to obtain the artifact. Although the raid failed to turn up the stone, Ghetsis managed to trick Black into revealing the entrance to the secret room where the Dark Stone was hidden. In Finding Truth, the stone was delivered to N at the Dragonspiral Tower, where he awakened Zekrom from it and converted it to his side to become the Hero of Ideals.
In PS543, after Ghetsis had obtained the DNA Splicers, he ordered Kyurem to absorb Zekrom, turning both Zekrom and N on its back into the Dark Stone. Although the stone was subsequently absorbed by Kyurem, N was soon expelled from it.