Naota gets run over by a mysterious woman on a Vespa, and grows a ridiculously large bump on his forehead.
Mamimi and Naota idling near the river
The episode begins with a sixth grade boy in a blue jacket, Naota Nandaba, and a much older high school girl, Samejima Mamimi, making small talk under a bridge near the edge of the river. Mamimi, who is the ex-girlfriend of Naota's brother, tries to show Naota how to swing, but he is not impressed and continues doing his homework. She then cuddles around him, and says that she must do so in order to keep from overflowing. Looking startled, he complains about her smelling like cigarettes. They both lie there for a while. In a narration, Naota claims that "nothing amazing happens here, and everything is ordinary. He mentions a large industrial complex in the middle of this rather small town called Medical Mechanica. The elders are proud of its inclusion in the community, but he sees the smoke it produces as an "omen."
Haruko running over Naota
Naota and Mamimi are seen on top of the bridge buying a drink. Despite Naota disliking sour drinks, she buys one anyway. A pink-haired woman with a large blue guitar on a vespa views them from afar. Angered by her drink choice, Naota begins to say something about his brother, but he notices a whirring sound. The lady with the vespa slams into Naota. She apparently wanted to stun him, but ended up killing him. The vespa woman immediately performs CPR, and by logical conclusion, busts him upside the head with her guitar. He comes to and barks at the woman, who calls him "useless" before speeding off.
Naota examining his bump
At home, Naota examines the red mark on his face, which has progressed into a oddly rectangular bump. He is able to push it down, but it simply pops back up. He covers it with a bandage. At school, his classmates talk of a vespa woman whose sting leaves a "demon's mark that show you've been doing naughty things." They proceed to annoy him about his obvious bandage, claiming that he must be perverted. In narration, Naota agains states the mundane atmosphere in his town.
Haruko assaulting Naota in the hospital
Naota stands at a railroad crossing as he makes his way to the hospital. He claims not to want to think about the vespa woman, but she then appears beside him. She begins to slyly ask if anything happens. He wants to be left alone, but while she goes on and on about his bump, he runs away. Naota is seen in the hospital in a dimly lit room, as a nurse in the foreground explains his condition. "Flyptonic Clipple Waver Syndrome. A disease that children get from trying too hard." Naota is immediately suspicious of this, and the nurse's voice morphs into that of the vespa woman. She asks for the truth then takes a swing at his head with the guitar. He is able to dodge this and other unseen blows as the hospital bangs around. He finally makes his escape.
The episode becomes a frantic manga for a while
Naota, back at home, is talking on the phone to Mamimi. He claims to have seen no photos and that she should leave him alone. He goes to dinner and is shocked to see the vespa woman having dinner with his father, who runs a bakery from home, and his grandfather. The show is temporarily portrayed in a dynamic comic manga format. They ask him to calm down and meet the new housekeeper, Haruhara Haruko. His dad claims that she ran him over, but took a liking and allowed her to stay. Haruko gossips that she saw Naota with a high school girl making out. Naota admits it was Mamimi after being smacked around by his dad. The father now assumes that his son is "Fondling around, fooling around..." even though there is no evidence. They begin using the term "Fooly Cooly" to suggest promiscuous behaviour.
After taking a bath, Naota finds Haruko in his room. She is seen talking to an unknown person, saying that "the channel is imperfect" and that "the kid I found is pretty useless." He confronts her about her business with her family, but manipulates the tense situation in her favor, constantly asking about what's hiding underneath the bandaid. He then yells at her, saying that she should know what's on his head since she hit him. He goes downstairs and his dad call him to the kitchen. The father wonders why they were both run over by the same person, and mentions that Mamimi came over to buy all of their stale bread. Naota becomes wide-eyed and runs to the river. Mamimi back on the bridge, smoking a cigarette with "Never Knows Best" scrawled on the side. Naota asks if she has had direct contact from his brother since he left. No reply. He then asks how much she likes his brother. She claims to like him as much as "watermelon, or like a panda with a mean face..." but she ultimately defines her affection towards him as "I like him more than hard bread." Naota, while being wrapped around the neck by Mamimi, tells her of his brother's new blonde girlfriend in the US. Simultaneously, Haruko ogles picture from his brother. Her chain bracelet begins to twitch.
FLCL Episode I Spawngate
Mamimi then stumbles around while holding her head, claiming that she is "going to overflow." Naota is confused, then freaks out as his head pulses and the bump begins to squirm furiously under the bandage. Its nearly triples in length. Haruko puts on her gear and makes a dash for the bridge. Medical Mechanica begins to beam with light as a siren sounds. Suddenly, a red robot and a white robotic hand form out of Naota's head and push each other before finally breaking off. Naota's shirt somehow gets stuck to the red robot as it climbs up on the bridge's support beams for battle.
FLCL Episode 1 Battle
The robot and the white hand wrestle around, but the robot has no real struggle in defeating its opponent. It tears out the wiring of the hand while Naota hangs back in confusion and awe. Haruko finally makes it to the scene. She revs up her guitar and, with delight, smacks the red robot in the head, which turns it blue. In narration, Naota claims that Haruko looks like his brother. The next day, everything is back to normal. Haruko instructs the robot on making bread. Naota meets up with Mamimi near the vending machine. She buys another sour drink and he takes it despite his wishes.