Shadow Pokémon are Pokémon whose hearts were corrupted and locked behind several "doors" keeping the light from their heart from shining through. Constant care and battle are needed to unlock the doors to the Pokémon's heart. After all the doors are unlocked the player can then purify the Pokémon using the Relic Stone in Agate Village or the Purification Chamber in the Pokémon HQ Lab. In battles, the shadowy aura buffets all Pokémon except those with the Shadow type.
Cipher created each Shadow Pokémon from his lab located close to the center of the Orre region. In the lab, Ein tried to perfect the formula for a Pokémon that was not afraid to attack other trainers. Once he found out that each Pokémon's heart could be locked away, he used this to create the Shadow Pokémon, perfecting his formula. However, due to the amount of corruption flowing from the Pokémon, it is possible to tell the difference between a normal "Pure" Pokémon and a "Shadow Pokémon". Only certain eyes can catch the strange, dark aura coming from them. Cipher took the S.S. Libra in order to take the Pokémon onboard and take them to the Cipher Key Lair to turn them into Shadow Pokémon.
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