Pokémon Colosseum puts significantly less importance on the non-RPG aspects of the game than Pokémon Stadium and Pokémon Stadium 2. For example, there are no minigames, nor is there a Gym Leader Tower. While it is the first 3D Pokémon video game with an RPG mode, it doesn't allow the player to use rental Pokémon the way the Pokémon Stadium games did. This was probably done because Pokémon are obtainable in the RPG mode, thus most of the features in the game are still usable without a Game Boy Advance Pokémon game or rentals. This title features support for the Pokémon Ruby, Sapphire, Emerald, FireRed and LeafGreen games.
It features all 386 known Pokémon as of the third generation. The game features a first for the Pokémon series, a true 3D role-playing game mode that allows the player to capture Pokémon that cannot be captured in the Pokémon Ruby/Saphire/Emerald game generation, allowing them to eventually be transferred into said games. This includes Legendary Pokémon such as Ho-oh, Entei, Raikou and Suicune. It also adds a new Pokémon status, Shadow Pokémon, in which this game's plot revolves around. These Pokémon can't be traded to any game until they lose their Shadow status, and are effectively forbidden from use outside the Story mode until purified. These Shadow Pokémon after being purified by the player will have special movesets that are not possible to obtain under regular circumstances.
The game takes place in the Orre Region, a barren desert wasteland overrun with crime. It begins with Wes (the main character, whose name can be changed by the player) planting a bomb in the Team Snagem (a minor antagonist) hideout and racing out as the place explodes. Wes also steals a miniature Snag Machine. Shortly after the explosion, the news network reports that the large Team Snagem "Snag Machine" was destroyed on the explosion and that the smaller, miniature version has been stolen. The latter is of particular concern because it allows the user to steal other trainers' Pokémon. The newscaster ends with the hopeful remark that the Snag Machine will not be used for criminal purposes again.
Meanwhile, as Wes enters Phenac City, he sees two suspicious-looking men attempting to haul a bag to the mayor. They spot Wes and challenges him to a battle. After he wins, the men flee, and Wes unties the bag to reveal a girl named Rui (again, whose name can be changed by the player). Rui is happy to be released and tells Wes that she can see a dark aura around some Pokémon, which is why the two thugs attempted to kidnap her. The two of them go to the mayor, named Es Cade, who questions Rui's sightings but promises to help them out.
Along the way, Wes and Rui track down these suspicious Pokémon. From picking up a set of items known as the Ein Files, they learn that Shadow Pokémon are Pokémon whose hearts have been artificially closed. Often when Wes enters battle, Rui spots the Shadow Pokémon and alerts Wes, who can then use his Snag Machine to capture them. Along the way, they meet a number of admins, who hail from a criminal syndicate called Cipher. Wes and Rui defeat the four of them and trace the syndicate back to the head boss.
Finally, Wes and Rui arrive at Realgam Tower. After facing the four admins once again, Wes obtains the key cards to reach the top of the tower. There, he is greeted by a large crowd, and a man named Nascour who then tells Wes that he will have to repay all of the debt that he had inflicted on them. After Wes defeats all of the trainers and then Nascour, Nascour attempts to save face, only to be interrupted by Es Cade. Es Cade reveals himself to be Evice, the secret head of the Cipher organization, and battles Wes. When Wes defeats him, Evice attempts to escape by helicopter, but the Legendary Pokémon Ho-oh swoops in and blasts it out of the sky.
Later on Wes and Rui are told that a new snag machine is at Team Snagem's hideout. They head there to destroy it but finds that it was a false story. Also, after getting 47 Shadow Pokémon, you are allowed to battle Team Snagem's boss, Gonzap, again. Then, at Outskirt Stands, there is a person who looks exactly like Wes and is attacking someone. After he is defeated, he can be talked to again and he reveals he is a Cipher Peon.
Shadow Pokémon are Pokémon that have had there hearts closed. They have been turned into fighting machines, and will attack even humans.
These Pokémon are created by Cipher.
There is only one girl that can see if a Pokémon is Shadow or not. If it is Shadow, you can catch it by throwing a Poké Ball at it with your Snag Machine, which is taken from Team Snagem at the beginning of the game.
How to Purify Shadow Pokémon
In Agate Village, there is a spot inside of a forest called the Purification Relic. If a Pokémon has all of the bars cleared, it may go and be purified by Celebi.
An item called a Time Flute can also be found. With a Time Flute, go to the relic, and your Pokémon do not have to have all of the bars empty. You can use it, and Celebi will come purify your Shadow Pokémon. That should mainly be used for the really tough/impossible ones to get the bars empty. There are 3 Time Flutes in the game, so use them wiseley because once they're gone, they're gone.
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