The Dark Stone appeared in Black—Victini and Reshiram and White—Victini and Zekrom. As the embodiment of Zekrom, the Dark Stone can glow blue from Zekrom's electricity. It first appeared under the ownership of the Hero of Ideals, as the hibernating form of the fatigued dragon Pokémon. The stone was hidden below the Sword of the Vale by the hero. In White—Victini and Zekrom, Ash awakened Zekrom from the Dark Stone to fight Damon's Reshiram; in Black—Victini and Reshiram, Damon was the one who found and awakened the Dark Stone so he could recruit Zekrom to his cause.
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 Dark Stone initially resided at the Desert Resort, where it was found and excavated by Clay and his mining team in Lights, Camera...Action!. After investigating the stone, he felt worried and called Lenora to come and investigate them with her expertise on ancient artifacts. As such, Lenora took the stone to her museum. Later, she called Drayden to help her investigate the stone, which helped them realize that it was actually Zekrom.
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 Abyssal Ruins, 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. In Giant Chasm, Kyurem ejected the Dark Stone from its body in order to absorb Reshiram instead. Zekrom reemerged from the Dark Stone soon afterwards.