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Shadow Pokémon
The main focus of the game, like its predecessor, is to capture Shadow Pokémon and eject them. Shadow Pokémon are captured using the Snag Machine, as in Pokémon Colosseum. In this game there are 83 different Shadow Pokémon to eject.[1] Each Shadow Pokémon has a set of Shadow moves that it knows to give it more variety in combat, which is a significant change from Pokémon Colosseum. Shadow moves can be either physical or special, which is the only type of move that was capable of this in Generation III. This changed once Generation IV brought physical and special moves for each type. These moves often have lower power than their non-Suspicious counterparts, but still inflict more damage due to being super effective. Their usefulness is also increased by not having to use PP when you use a move, as they can be used as often as needed within a single battle.[2] If at some point in the game the player cannot catch a Shadow Pokémon, there is a second chance available: at random points throughout the game an antagonist, Miror B. will appear and have a Shadow Pokémon that the player was not able to catch.[3] Once the player has obtained 82 of the Shadow Pokémon, Miror B. will appear one final time with the final obtainable Shadow Pokémon in the game.[4]

Purifying Shadow Pokémon
Once a Shadow Pokémon is captured the player then has to purify it. There are two different ways of purifying Pokémon: one way is to use the Purification Chamber,[5] and the other is to carry the Pokémon in the party just like in Pokémon Colosseum. The Purification Chamber allows the player to place anywhere from 1 to 4 Pokémon in a circle and a Shadow Pokémon is placed in the center of this circle.[5] Depending on the Pokémon that are placed in the circle the tempo will increase, which increases the speed of purifying the Shadow Pokémon.[5] After that the Shadow Pokémon will be purified as the player walks around, and they will be notified when a Shadow Pokémon is ready to be purified.[5] When the player carries the Pokémon in the party and battles with them, they will gain experience when they are purified. If the Purification Chamber is used then the Pokémon will not gain any experience, but with the Purification Chamber multiple Pokémon can be purified at the same time.[5]

Mt. Battle
The Mt. Battle area is an area that is accessible early on in the game and is a 100 trainer challenge.[6] The 100 battles are split into 10 battles in 10 different zones with the trainers in each zone being stronger than the ones in the zone before.[6] The tenth trainer in each zone is called the Area Leader, and after each Area Leader is defeated the player gets a specific number of pokecoupons.[6] When the player defeats an Area Leader the first time the player gets a special item.[6] At the front desk Mt. Battle the player can exchange their pokecoupons for certain prizes.[6]

Poke Spots
One other new aspect to the game is that there are three different PokeSpots throughout the game.[7] At these special locations the player can lay Poke snacks in the area to cause wild Pokémon to appear.[7] At these 3 locations 9 different wild Pokémon can be captured and they can be traded for rare Pokémon.[7]

Story
See also: List of Pokémon characters and List of Pokémon
The story begins five years after the events of Pokémon Colosseum with the introduction of The Hero (named Michael by default) as the main protagonist. Michael talks to Professor Krane, his mother's boss, who introduces the concept of Shadow Pokémon, which are Pokémon whose hearts have been artificially closed. The criminal syndicate Team Cipher is creating and distributing them for their evil purposes. Krane also introduces the Snag Machine, which is used to capture Shadow Pokémon to purify.[8] Krane entrusts Michael with the Snag Machine to capture these Shadow Pokémon and is given the Aura Reader (the eye piece) to identify them from normal Pokémon.

Shortly after this, Krane is kidnapped by Cipher agents. Michael goes after the Cipher Agents to rescue Krane, and soon is led on many adventures throughout Orre. He must defeat the Cipher Peons and Admins and rescue the shadow Pokémon to save Orre from the evil Cipher. At the end of the game, he must get to Citadark Isle and battle the main villain: Master Greevil, who, in the beginning of the game, was thinly disguised as an old rich man named Mr. Verich. After Michael defeats Greevil and snags his shadow Pokémon, he must purify all of them, including the (seemingly) impossible to purify Shadow Lugia. After all of the Pokémon are purified, Michael returns home and puts down his snag machine, but he stores it safely in his room to be used if it is ever needed again.