FLCL revolves around Naota. His life in the city of Mabase is interrupted by the arrival of Haruko Haruhara (who is an alien) who bursts on the scene by running Naota over with her Vespa scooter, then giving him CPR and hitting him on the head with a blue vintage Rickenbacker 4001 left-handed electric bass guitar. Later, Naota is shocked to find Haruko working in his house as a live-in maid.
Since then, Giant Robots from Medical Mechanica have been coming out of Naota's head and cause more problems for Naota. Haruko is using Naota for her search for the Pirate King, Atomsk, because Naota's head is the only one that can create a passageway for the robots. It also puts her at odds with Medical Mechanica, the monolithic industrial corporation. At the same time, Naota is being watched by Commander Amarao, who believes that Medical Mechanica is out to conquer the galaxy. The combination of circumstances gets Naota involved in a three-way battle between Haruko, Amarao and Medical Mechanica. The underlying theme is Naota's coming of age as he becomes more mature and learns to express his feelings.