"FLCL Alternative" is a six-episode anime series that serves as a sequel to the original "FLCL" (Fooly Cooly), though it features a new cast and setting. The story centers on Kana Koumoto, a 17-year-old high school student navigating the challenges of adolescence in a small coastal town. Kana's life takes a surreal turn when she encounters Haruko Haruhara, a mysterious and eccentric woman who arrives on a moped and wields a bass guitar as a weapon. Haruko's arrival coincides with strange phenomena, including the emergence of giant robots that burst from people's heads, often triggered by emotional turmoil.

Kana and her close-knit group of friends—Mossan, Hijiri, and Pets—find themselves caught in the chaos caused by Haruko's presence. Haruko claims to be searching for the Pirate King, Atomsk, and uses Kana and her friends as pawns in her quest. As the series progresses, Kana grapples with her insecurities, fears about the future, and the complexities of her relationships. The narrative explores themes of growing up, identity, and the transition from adolescence to adulthood, all while blending absurd humor, sci-fi elements, and emotional depth.

The series maintains a balance between its episodic structure and overarching plot, with each episode delving into the personal struggles of Kana and her friends. The climax reveals Haruko's true intentions and her connection to the enigmatic Medical Mechanica plant, a recurring element in the "FLCL" universe. By the end, Kana gains a deeper understanding of herself and her place in the world, even as the story leaves many questions unanswered, staying true to the surreal and open-ended nature of the franchise.