Since the events of FLCL: Alternative, people are once again living their ordinary lives. Meanwhile, two frustrated teenagers hope for a major change.

In this prequel to the original FLCL, the youngsters accept the decline of the city as part of their reality until Haruko throws the city into chaos.

The series centers on the misadventures of 17-year-old Kana, a high school junior who spends her days hanging out with her besties, Mossan, Hijiri, and Pets. They live unremarkable lives, until the day a Mecha falls out of the sky, along with a strange woman named “Haruko.” Her plans for Kana and her friends involve the force known as “ATOMSK.” Kana will have to risk everything to decide whether or not to help… like she really has a choice!

Many years have passed since Naota and Haruhara Haruko shared their adventure together. Meanwhile, the war between the two entities known as Medical Mechanica and Fraternity rages across the galaxy. Enter Hidomi, a young teenaged girl who believes there is nothing amazing to expect from her average life, until one day when a new teacher named Haruko arrives at her school. Soon enough, Medical Mechanica is attacking her town and Hidomi discovers a secret within her that could save everyone, a secret that only Haruko can unlock.

When Haruko runs over Naota with her scooter and brains him with a bass guitar, his world doesn’t just get turned upside down—it gets incredibly weird.