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According to the Unova legend, Zekrom was once part of a single Dragon Pokémon. Two brothers used it to created the Unova region, but when they argued about how to rule the Pokémon split in two. Zekrom sided with the younger brother who pursued ideals, the elder brother who pursued the truth had Reshiram side with him. Sometime after the battle of the brothers, Zekrom was turned into the Dark Stone.
Zekrom was first seen sealed within the Dark Stone and situated from the Desert Resort to Nacrene City along with the Light Stone. Shadow Triad and a Team Plasma Grunt disguised as Brycen tricked Black into revealing the location of the Dark Stone and then they stole it. The stone was brought to Ghetsis who brought it to N. N then revived Zekrom at the Dragonspiral Tower, but then it started to attack N. However, N was able to calm Zekrom and the Deep Black Pokémon decided to choose N as the new Hero of Ideals.
N did not use Zekrom in his battle against Alder, nonetheless he managed to defeat the Pokémon Champion. After Black managed to awake Reshiram in True Friends after get mad that Cheren was manipulated by Team Plasma, N and Zekrom came out with the rest of the team and attacked Black and the Pokémon League. Although he initially struggled, Black managed to defeat Zekrom with Fusion Flare powered up by Fusion Bolt. When they fly back to N's Castle, a second Zekrom suddenly appeared. It was actually N's Zorua, N actually released him along with his other Pokémon minus Zekrom, but Black revealed that it wanted to stay with him. After Black defeated Ghetsis, N flied off on Zekrom, leaving Zorua behind, to follow his own path.
N was seen flying on Zekrom chasing the Light Stone which contained Black. They caught up to it in the Entralink where it was found by White. She asked N why Zekrom didn't change back into the Dark Stone like Reshiram but N didn't know the answer. Zekrom then got drawn by the presence of Kyurem whom it then proceeds to battle with N and Ghetsis.