From Bulbapedia, the community-driven Pokémon encyclopedia.
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The version mascot of a Pokémon game is the Pokémon that appears on the boxart—and often label—of that game.
Early on, the version mascot of a game was not necessarily relevant plot-wise, and did not have to be even met to complete the game. Generation III (with the exception of the Generation I remakes) began the trend of the version mascot being mandatory to encounter in order to progress the plot, and more recent games even force the player to catch the mascot to continue. Version mascot Pokémon are often given increased catch rates and the ability to respawn if they are defeated in order to account for this. All version mascots after Generation I have been Legendary Pokémon, barring Generation I's remakes.
In general, only core series games have version mascots, as most side series and spin-off games display multiple Pokémon on their box covers and so none of them qualify as mascots. The only current exception to this is the side series game Pokémon XD: Gale of Darkness.