新手训练家小智从大木博士那里获得的是一只勉勉强强又喜怒无常又不喜欢进入神奇宝贝球的皮卡丘，小智离开家乡真新镇，在关都地方展开他的旅程。在赢得皮卡丘的信任后，小智认真地开展他的旅程来挑战各地的道馆，参加神奇宝贝联盟。在旅途中加入小智的是两位良师益友——小刚和小霞。参加石英大会之后，小智受大木博士之托启程前往橘子群岛，从内木博士处取得GS球，小刚暂时留在内木博士处。旅途中小智参赛橘子联盟，还遇到神奇宝贝观察家小建。回到真新镇后，大木博士无法理解怎么样把GS球打开，所以就把小建留下做助手，派小智、小霞、小刚前往城都地区，把GS球交给桧皮镇的钢铁先生。再次，小智参加了神奇宝贝联盟－城都联盟的白银大会。
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