Sixteen years ago, a mysterious masked ninja unleashes a powerful creature known as the Nine-Tailed Demon Fox on the Hidden Leaf Village Konoha, killing many people. In response, the Fourth Hokage Minato Namikaze and his wife Kushina Uzumaki, the Demon Fox's living prison or Jinchūriki, manage to seal the creature inside their newborn son Naruto Uzumaki. With the Tailed Beast sealed, things continued as normal. However, in the present day, peace ended when a group of ninja called the Akatsuki attack Konoha under the guidance of Tobi, the mysterious masked man behind Fox's rampage years ago who intends on executing his plan to rule the world by shrouding it in illusions.

“我对普通的人类没有兴趣。你们之中要是有外星人、未来人、异世界来的人、超能力者，就尽管来找我吧！以上。”这位就是在开学的自我介绍中，发言惊爆的凉宫春日。对于平淡无聊的日常生活无法忍受的她，创立了一个不可思议的社团——让世界变得更热闹的凉宫春日的团，通称SOS团。 虽然同班同学阿虚、寡言读书少女长门有希、萌萌学姐朝比奈实玖瑠、神秘转校生古泉一树等人都被她牵扯进来，但是阿虚以外的三人却有着凉宫春日不知道的大秘密。