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The story begins with a cut-scene where the {{player}} is to have been unconscious on a beach due to a time-traveling accident, causing him/her to become a Pokémon. Meanwhile, the partner is nervous about joining the [[Wigglytuff's Guild]], a local exploration club, and gives up early. Walking along the beach, the partner encounters the player, and informs that the player has been turned into a Pokémon. The [[Relic Fragment]] the partner holds is then stolen by {{p|Zubat}} and {{p|Koffing}}, members of [[Team Skull]], which the player helps recover. After a brief exchange, the partner explains their motivation for joining the guild. The player's partner loves legend and lore and their life dream is to find the secret of their personal treasure-atreasure—a Relic Fragment with a strange pattern on it. The partner, reinvigorated by the player's courage, joins the Guild as a new team with the player.
Over the next few days, the team gets accustomed to life at the Guild and the nearby [[Treasure Town]]. Among the folks they meet are {{mdc|Wigglytuff|2}}, the kindhearted Guild Leader, {{mdc|Chatot|2}}, the hot-tempered yet well-meaning second-in-command, {{mdc|Bidoof|2}}, the newest recruit prior to the team joining, the Guild chef {{p|Chimecho}} (also in charge of maintaining the team), {{p|Diglett}} and {{mdc|Loudred|2}}, the Guild sentries, {{p|Dugtrio}}, maintainers of the job boards, {{p|Magnezone}}, the local sheriff, and other exploration teams. As they are introduced to the Guild, they learn of the fact that rogue Pokémon have been wreaking havoc in the world due to the disruption of time, Pokémon cannot [[evolution|evolve]], and new "Mystery Dungeons" have been revealed and open to exploration.

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