Pikachu and Piplup are introduced to Wish Park, a mysterious dimension accessed through portals in each region of Poképark, and quickly realize that it is a trap designed to entrance the inhabitants of Poképark. They allude to a "light among the darkness" as Pikachu arrives at Seasong Beach of the Cove Area, the opening area of the game, with his friend Piplup. The game opens with the Legendary Pokémon Reshiram and Zekrom conversing about a new threat to Poképark. Upon defeating an opponent, they will typically befriend the player and be added to the 'Pal Pad', which lists information about all the Pokémon in the game, and will aid the player in opening the Poster Portals which serve as the entrances to Wish Park, the location of the main antagonists of the game. Other Pokémon will sometimes offer other challenges such as quizzes or Hide-and-seek. In battle mode, the player must defeat their opponent in combat.
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In chase mode, the player must tag the opponent within a time limit. Various Pokémon encountered throughout the game will challenge the player to a handful of games. The player uses one of four Pokémon available, Pikachu, Oshawott, Snivy and Tepig, and can switch them out at will each Pokémon has their own special abilities. PokéPark 2: Wonders Beyond is primarily singleplayer, with the exception of the attraction minigames which feature multiplayer capabilities for up to four people.