At the risk of sounding like a bait-and-switch, FLCL's story does matter, but for very different reasons than people often discuss when the show comes up. It isn't a show that's always easy to follow, making some people label it as something that has some merit but is utterly nonsensical without a lot of a point.
Kazuya Tsurumaki's FLCL, or Fooly Cooly, is about a young boy named Naota living in a town where "nothing amazing happens." That is, until a woman on a Vespa bashes him in the head with a base guitar, uprooting his everyday life and causing robots to spawn out of his forehead, making his already confusing adolescence all the more complicated. Even the above paragraph is only a fraction of the experience over six short-but-sweet episodes stripped down to avoid an unnecessary presumption or over-encumbrance of detail. By the end of FLCL, a lot has happened, and many viewers will miss stuff the first time, and this can lead to all sorts of assumptions.
Theory: It's All Nonsense
Broad reactions to FLCL fall into two categories: those that think of it as an incredibly deep and rich narrative experience and those who think of it as just a ride. There are few who are likely to have seen it who won't heap it with some praise, namely regarding its music by The Pillows, as would anyone. Even so, consider the school of thought that FLCL doesn't have a real story. What might support that?
Perhaps it's how many questions the viewers have throughout the first viewing and maybe even at the end. Things like "what's Atomisk?", "what is Medical Mechanica?", or "what exactly is Haruko's goal?" And a lot of these questions have answers, but not all are apparent or without some room for interpretation.
Conjecture: The PLOT Doesn't Matter
Stories - especially in visual mediums - can be divided into different kinds of texts simultaneously present throughout. There is - of course - text and subtext. "Text" refers to what is conveyed clearly to the audience. "Subtext" refers to hidden or implied information in the text, inferred by patterns therein. Through subtext comes context and from that, themes become associated with the story as a whole.
The text itself can be divided among itself as well, and within there are the lore, plot, and mechanics of the series, but also the character stories that tend to dominate more of the screen-time. Among the plot of the series, there are elements like the following:
- Medical Mechanica
- The "N.O." portals in Naota and other characters' heads
- Atomisk
- The Bureau of Interstellar Immigration
These are the things most people will likely have questions about. They'll wonder what Medical Mechanica even does, what Atomisk does, and why the guy with the big eyebrows and his people are so interested. And these elements, in the grand scheme of the story, do not matter.
Subtext & The Meaning of FLCL
FLCL's most common interpretation is that it's a show about puberty and growing up, signified adequately by the fast pacing and melodramatic flare that reflects how adolescence feels. This is further expressed by Naota's childish crush on Haruko and his lack of solid adult role models.
In episode 2, Naota talks about learning the truth about things, signifying that a big struggle of his adolescence is about parsing truth and lies among grown-ups, who he sees as immature. Naota wants to grow up so badly that he ends up missing out on being a kid. And this insane adventure he goes on is like the universe teaching them to live a little and to enjoy the lies of being young.
Those plot points that "don't matter" still serve a purpose, but only in the capacity of what they represent, not in regard to the characters. It makes no difference what Medical Mechanica actually does, just that it is a vague antagonistic threat that symbolizes power, just like Atomisk, the almighty power that Haruko is hunting.
Every single one of the six episodes, no matter how the plot progresses, is about the characters first and foremost. The first episode doesn't explain a single thing but builds up to a climax where Mamimi has a panic attack after learning that Naota's brother has a girlfriend in America. The second episode is all about Mamimi's past, then the third is about Ninomori, and so on.
Story vs Storytelling
There is the old adage that it's not as much about the story as how you tell it and that couldn't be more true with FLCL. It is a story that in many ways operates on emotion and elicits as many reactions as possible, through music and visuals. These things have been praised up and down for years, but just because something looks good, is it a good story?
It depends on if and how someone separates the story from how it is delivered. Perhaps the story should be judged by its written form as a screenplay? But then that's changing the medium by which it is presented, and different mediums must be judged by different metrics. Since it is technically an adaptation of a manga, one could compare the two, but that seems irrelevant. FLCL is an anime and by all accounts, it is an exceptionally well-made one.
Through voice acting, music, sound effects, animation, direction, and screenwriting, the story comes to life. If a story succeeds at capturing the viewer's attention and getting them invested in the emotions of a scene, it has succeeded as a story. But FLCL was never just important because it had a meaningful story. It's also one of the most impressive anime ever made.
What It Is To Be Fooly Cooly
Kazuya Tsurumaki and the animators at Gainax truly outdid themselves in these six episodes. Almost every creative decision, upon research, can be revealed to be either a personal anecdote about the creative team or something that was done to make the coolest possible thing. Every design, every odd visual gag was conceived because someone in the staff, usually Tsurumaki, "liked it."
Furthermore, there are moments of animation in FLCL that are so unique, vivid, and gorgeous, that almost nothing else has come close to replicating it. There are these 360-degree rotating cuts done in a blend of 3D and 2D that look better than most 3D anime out of Japan in the next two decades. The list of eccentricities goes on, but the simple fact is that FLCL just hits different.
In episode 1, during the famous manga sequence, there is a fast-paced, obtuse conversation between Naota, his father and grandfather, and Haruko, where the term "Fooly Cooly" is coined. It's utterly nonsensical, and the characters can't seem to come to a consensus on what it means.
That conversation best sums up what trying to sum up FLCL is like. It's so many things, both simple and complicated, to so many people. For those that haven't watched it, it's best to remember that it's a show that demands a rewatch to fully absorb it. Whether it takes months or years to appreciate it, eventually everyone finds their own meaning to the term "Fooly Cooly."