Underneath all of the complex and intertwining layers of uniquely converging and intertextual media styles, the basic story of FLCL is that of Naota coming of age. No matter what happens in his secluded world of Mabase, Japan, he is still a liminal 12-year-old boy looking for answers in a world filled with questions. Should he follow his brothers lead and accept an American influence or go even farther and be swayed by the alienness of Haruko? Or should he perhaps stick to one of the more native tracks like the traditional Japan personified by Mamimi or the upper class of Ninamori?
Many events during the course of the series show Naota as taking those steps necessary to break through his liminality and finally be able to make the decision which will affect the rest of his life as well as the direction of liminal Japan. Naota has saved Mabase from a rapidly approaching meteor through the use of his newly acquired baseball skills which finally caused the townspeople to notice him for who he is instead of as Tasukus brother. He learned to force himself to drink sour drinks even though he hates the way they taste and even is able to eat super spicy noodles, the likes of which most adults cannot handle. Naota has dealt with his feelings for Mamimi, and even tried to initiate a kiss with her, only to be turned down, but he learned from this event.
He freed Atomsk from the trappings of Medical Mechanica and in the process saved Mabase a second time, here from the fate of enslavement due to ironing out the wrinkles of their brains. Naota has made peace with his mother figure even though she left him alone again, and even managed to tug the heartstrings of an alien. In the ultimate act of putting himself out on a limb, he tells Haruko he loves her and gives her a kiss.
In the end, after overcoming all of the traumas he has been forced to deal with and even the ones that he created for himself, Naota realizes that he does not have to decide just yet. There is still time and he chooses not to choose. He will remain a kid for a little while longer and let the events of the future help him decide what kind of person he truly is to become. He is seen in the last moments of FLCL wearing his new middle school uniform and deciding definitively that he does not like sour drinks, and is not ready to force himself to drink them. In much the same way, Japan itself has no real need to make a decision immediately on its place in the world of the 21st Century. It can remain content in its current place in the world stage. Its time will come.
