小智为了参加神奇宝贝彩幽大会，努力挑战道馆，丰缘联盟结束后，则动身挑战故乡关都地区新设的对战开拓区。而小遥则以成为协调训练家努力，挑战各地的华丽大赛。故事中的反面角色由火箭队二人组增加到火岩队和水舰队。相比略带搞笑色彩的火箭队，火岩队和水舰队则显得更加“专业”。小智等人与其对抗，并见证超古代神奇宝贝力量的经历也成为了故事的另外一条线索。在此系列中，无印篇的女同伴小霞不再跟着小智，而橙华市的新手训练家小遥加入队伍。小遥本来只打算旅行，但得知神奇宝贝华丽大赛后，就决定成为协调训练家。小遥的弟弟，小胜也跟着他们旅行，还带着神奇宝贝领航员。不过，因为小胜年龄不足，所以没有神奇宝贝。小智的伙伴，小刚也在此系列的开端回来。小智与小刚都以新装登场，小智也没有戴着旧帽子，并且穿着完全不同的新行装。小霞在超世代中也曾客串，同样穿着新装。展开全部收起全部
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