主人公久远寺睦是巡回马戏团的一员，某日他们来到了天空中有鲸鱼游弋的城市，而他在鲸鱼之丘上遇见了神秘的鲸鱼少女的故事，随着美少女们一个个登场主角久远寺睦也开始忙碌起来。但这个城市背后到底有着什么故事呢？

Like snow falling in summer, like a cicada lamenting the coming of winter... In a town watched over by a whale in the sky... the extraordinary is made ordinary. Spectacles that could never be given form are instead given flesh and soul. And in their midst, the story of a miracle that comes to pass in this town of miracles incarnate... For Kuonji, this newly-discovered vision is a thing of wonder and fright – a sentiment not shared by his peers. Under its watchful gaze, Kuonji chats with and hangs out with his somewhat unusual friends. Whether it's with Nina and her striped panties, cat-loving Sacchan, the strange alien Allen or a variety of other busty, skimpily-dressed babes, Kuonji finds himself in the middle of ecchi situations galore! Welcome to the world of Final Examination Kujira.