The first season covers the story of a sixth grade student named Naota Nandaba whose life is greatly changed after he is run over by the mysterious alien troublemaker Haruko Haruhara.
During the events of FLCL Alternative, claiming to represent the Galactic Space Patrol Brotherhood, Haruko directly antagonizes Medical Mechanica while entering Kana Koumoto's life to gauge the potential of her latent N.O.
From Kana's forehead she acquires a red 1968 model Fender Mustang, and she is not seen until the finale riding her signature Vespa SS 180, which is left in the care of noodle chef and occasional accomplice Dennis Yoga.
Haruko was ultimately sucked through the "Naked Focal Point", a giant wormhole opened by Kana unleashing her full power to end Medical Mechanica's apocalypse event.
She uses Shinpachi's NO Channel to acquire a weaponized midnight blue left-handed Rickenbacker bass guitar model 4001 that fire bullets and has axe and rocket launcher modes.
During the first season of FLCL, having come to the planet years before and having a history with Amarao, a deemed failure to her expectations, Haruko arrives to Earth under the cover of an investigator for the Galactic Space Patrol Brotherhood to find a human with N.O.
She eventually finds Naota and established the channel by hitting him with her guitar, moving into his household as a maid to keep tabs on him while her constant presence endangers him and others on a daily basis.
Haruko eventually devours Julia, restoring her original hair color, and focuses her full attention on a defiant Hidomi whom she provokes into attacking her just as Atomsk approaches Earth.
She also wears a set of cat ear headphones which Julia Jinyu recognizes to be an inhibition device created by Medical Mechanica that protects her from both her own power and Haruko's mind altering abilities.
Once the factory is destroyed, gaining glimpses of Haruko's attempt to contain Atomsk and her intent with that power, Hidomi refuses to help as she became a different person to the point that her dreams are no longer morbid in nature.
In the latter case, a conscientious attempt to satisfy Shigekuni's request, the manga states the robot would spend three hours at a time looking through "perverted magazines" which gave the impression that he likes porn.
When Mamimi first saw the robot while he was wearing a halo and wings, believing him to be a god due to his angelic appearance, she named him "Canti" after "Cantido, the Lord of Black Flames" in the video game she plays.
Despite his appearance, Canti expresses human-like emotions as he feels embarrassed about his broken head (where Haruko hit him) and spends his free time finding the pieces to glue back together while wearing a box.
In the final episode of the first season, his monitor displaying the characters for "child" (小人) instead at the time, Canti is revealed to be a component piece of the Medical Mechanica's Terminal Core and used by both the organization to power their doomsday device and Haruko to complete Atomsk's arrival to Earth.
However, the robot is eventually discarded and sent to the organization's space base, his severed head coming back to life as a dog-like creature as the result of Atomsk's arrival to Earth while ingesting Ide's being.
Amarao first appears in the original series to covertly warn Naota of Haruko and her intentions, giving viewers the impression that he is virtually an omniscient character with his dispensing of background information and fairly accurate predictions.
He made a cameo appearance in FLCL Grunge, having hid away under the junkyard near Okura and flying off with Haruko hitching a ride on the Medical Mechanica plant as it pursue him, with the company eventually capturing Atomsk.
Medical Mechanica (メディカル・メカニカ, Medikaru Mekanika) is a mysterious organization that serves as a secondary antagonist in the FLCL series, being of alien origin like Haruko and seeking Atomsk's power for their own agenda.
Having placed a clothes iron-like factory on Mabase, its bottom outfitted with a laser cannon, Medical Mechanica's goal is said to be ironing out the wrinkles in both a figurative sense and as a literally means of terraforming.
In FLCL Progressive, traces of their presence on Earth are still seen, Medical Mechanica is revealed to have developed the earphones Hidomi wears as Haruko's actions once more cause conflict between it and the Interstellar Immigration Bureau.
Mamimi entered a sort of relationship with Naota as a means of coping with Tasuku having left for America and getting a new girlfriend, calling him "Takkun" before he realized she was using him and emotionally explodes about her using him as a consolation prize during the events of Brittle Bullet while vowing to win her love.
Naota, believing his father and Haruko are sleeping together, eventually learns the truth when he indirectly deactivated the robot and found the real Kamon whom he revived by being hydrated in their bathtub.
She projects herself as a proper and slightly stuck-up cynic with good grades while concealing personal information to an almost obsessive degree; like needing corrective lenses, instead wearing contacts while at school.
When news of her father's affair with his secretary is made public with the possibility of her parents getting a divorce, Ninamori rigged the classroom ballots to get the lead role in a Puss in Boots play while having Naota cast as the titular character to his dismay.
In this instance, a cephalopod-like Medical Mechanica robot which first appeared on Naota's head as cat ears transferred itself over to Ninamori at the time it begins to gradually manifest while using her body as a both a weapon and shield in its attempt to capture Canti before it finally emerged after ingesting curry and is destroyed.
While originally a part of Haruko, possessing a Fender Jazzmaster that was initially Naota's Gibson Flying V before it fused with Atomsk's guitar, Julia has a more serious and blunt personality and travels in a vintage Chevrolet Bel Air that can transform into a robot with multiple functions.
Marco Nogata (マルコ 野方) is a classmate of Hidomi's who is of Latino descent and Goro's friend, appearing to passively absorb the oddities of his class while becoming a part-time worker and test subject at the Interstellar Immigration Bureau's amusement park front.
Eye Patch (アイパッチ) is a homeless guy whose real name is unknown and is a member of the Interstellar Immigration Bureau, appearing in numerous places like as a regular at the Hibajiri café.
Masurao (マスラオ) is Commander Amarao's son who serves as Eye Patch's aide, keeping his activities in the Interstellar Immigration Bureau a secret from Aiko by pretending to be a boxer.
Tonkichi (屯吉) is an elderly member of the Interstellar Immigration Bureau who works under the cover of an amusement park worker in a Mr. Dodo costume, hiring Marco Nogata to test a new attraction which is later revealed to be part of an anti-Medical Mechanica weapon.