- Colosseum Battle: Similar to Pokémon Stadium, this is the mode where you battle with a registered team (Either from Story mode or Pokémon Ruby/Sapphire/Emerald/Leaf Green/Fire Red). Unlike Pokémon Stadium, Colosseum battle is divided by Colosseums instead of cups. There are four colosseums of rising difficulty, 2 for Level 50 pokémon, and 2 for Level 100 Pokémon. Additionally, each Colosseum is playable in Single Battle or Double Battle mode. Victory (8 Battles) is rewarded with PokéCoupons.
- Mt. Battle VS 100: Similar to the one in Story Mode, this mode pits the player against 100 trainers of increasing difficulty. Every 10 battles there is a rest stop where you are awarded some PokéCoupons and given the option to take the coupons and quit. The Pokécoupons are only awarded if you choose to end the game at a rest stop or beats all 100 trainers. Also playable in Single or Double Battle modes. After beating the 100 trainers and having caught and purified all Shadow Pokémon, Ho-Oh will be transferred into the PC, saying that it will give its service upon you.
- PokéCoupon Exchange: PokéCoupons are awarded for completing Colosseum or Mt. Battle mode. This mode allows you to exchange the hard earned PokéCoupons for items, some of which can only be obtained this way. Note that using Legendary Pokémon in either mode reduces the amount of PokéCoupons earned.
This mode allows up to 4 players to fight against each other. The first player can either use the Story Mode team or their own from a GBA, but each additional player must have their own GBA to play. Custom Rules are available. 2 Player battles occur in Pyrite Colosseum, while 4 player Battles occur in The Under Colosseum.