A Shadow Pokémon has been turned into a souless fighting machine by artificially shutting off its emotions. Ein, the brains behind the Shadow Pokémon process, refers to this as "shutting the door to their hearts".
Shadow Pokémon radiate a black aura that cannot normally be seen. However, Rui has psychic abilities that allow her to recognize Shadow Pokémon on sight. It was for this reason that she was kidnapped by members of Cipher.
The overwhelming power of Shadow Pokémon causes them to behave oddly and irrationally. This feral state is called Hyper Mode.
Pokémon in Hyper Mode will ignore orders, and sometimes turn on their own trainers. While a Pokémon is in Hyper Mode, Shadow Rush will hit critically more often.
However, Hyper Mode prevents the use of items on the deranged Pokémon. Calling the Pokémon by its name will return it to its senses and end Hyper Mode. Doing this also causes the Pokémon's heart to open a little.
There are several ways to purify a Shadow Pokémon; their effectiveness varies according to the individual nature of a Pokémon.
As the process continues, the Shadow Pokémon slowly regains its original moves and personality. When a Pokémon is finally purified, it will gain all the EXP it has built up, along with a powerful move.
The time-traveling Pokémon Celebi has the power to enhance the purification process. When a Shadow Pokémon meets Celebi, its heart will instantly revert to its original form. A Time Flute can be used to summon Celebi and purify any Pokémon at any time.
Shadow Pokémon Information
Unused Shadow Pokémon
According to unused text in the game, the following Shadow Pokémon were originally planned for the game, but never used:
The role of Shadow Pokémon in Pokémon XD is unknown, however, screenshots appear to dictate that there are not only Shadow Pokémon present, that also the player can catch them. The main storyline centres around a dark Lugia.