[Wings of Fire]

As in Pokémon Gold and Silver, the primary Pokémon of the remakes are native to the Johto and Kanto regions. Due to advances in gameplay since the second generation, the regional Pokédex used in Gold and Silver (the New Pokédex) has been updated to include those Pokémon which evolve upon learning a new move. Rather than simply excluding these evolutions (as Pokémon FireRed and LeafGreen did with happiness-based evolutions), an improved Johto Dex was established with 256 Pokémon: five more than the New Pokédex.

Similarly to other recently released Pokémon games, Pokémon from outside the regional Pokédex can be captured after defeating the Elite Four and earning the National Dex. Pokémon native to Sinnoh and Hoenn can be found in various methods. Swarms of Pokémon sometimes break out across the Johto and Kanto regions; oftentimes these are not native to either of the regions. Pokémon from other regions can be located by playing one of two special stations on the PokéGear's radio function. There is a channel for Sinnoh Pokémon which plays only on Thursdays; the Hoenn channel only plays on Wednesdays. By having either of these programs turned on when in tall grass the chance of finding a foreign Pokémon increases. The Bug Catching Contest also hosts, from time to time, Hoenn and Sinnoh Pokémon. They will only appear on Thursdays and Saturdays. The Johto Safari Zone's customization option also allows for the finding of Pokémon from other regions.

In an apparent attempt to remove reliance on Generation III cartridges, starter Pokémon of Kanto and Hoenn can be obtained late in the game from Professor Oak and Steven Stone respectively. Some legendary Pokémon which were not included in the Generation II games, such as the legendary birds trio and Mewtwo.

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