FLCL revolves around Naota. His life is interrupted by the arrival of Haruko Haruhara, who bursts on the scene by running Naota over with herVespa scooter, then giving him CPR and hitting him on the head with a blue vintage Rickenbacker 4001 left-handed reverse strung 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 Meccanica have been coming out of his head and cause more problems for Naota and Haruko. Haruko is using Naota for her search for the Pirate King, Atomsk, which puts her at odds with Medical Meccanica, the monolithic industrial corporation. At the same time, Naota is being watched by Commander Amarao. The Commander believes Haruko is in love with Atomsk and that Medical Meccanica is out to conquer the galaxy. The combination of circumstances gets Naota involved in a three-way battle between Haruko, Amarao and Medical Mechanica.
