In a city called "Shuse" in Japan in the near future, the citizens live an ordinary life, but in a corner of the city, on the hill stands a factory built by a medical equipment manufacturer that looks like an iron. At a fixed time every day, the factory emits a lot of steam as if something has just been ironed. Naota, a sixth-grade elementary school student, and high school girl Mami, the girlfriend of Naota's brother who is studying abroad, spend time together by the river. It should have been an ordinary day, but it ended when the train driven by the legendary bee girl, Jingzi, hit Naota. Naota has a strange horn on his head! And Jingzi actually became a servant in Naota's house and entered Naota's house. Jingzi's secret and the meaning of "FLCL" that she often recites have brought about earth-shaking changes in Naota's life.