Fooly Cooly starts out with Naota walking home with his older brother’s ex-girlfriend, Mamimi. Out of the blue he is hit by an alien girl on a yellow Vespa bike carrying a 1976 Rickenbacker bass guitar. This all happens in the town of Mabase, dominated by the Medical Machine factory. The very next day Naota finds that the alien girl, Haruko, has been hired as the housekeeper at his father’s bakery.
Naota Nandaba, while walking with his older brother's delusional "girlfriend", seventeen year old Mamimi Samejima, is struck by a Vespa driver, who revives Naota and hits him in the head with her bass guitar before driving off. This turns it into an N.O. channel, from which objects and other beings can be pulled. Naota discovers a horn protruding from his head where he was hit, concealing it with a bandage. He keeps the horn secret from his classmates the next day and he goes to the hospital, where he again encounters the mysterious woman disguised as a nurse. He flees before she can strike him again with her guitar.
At dinner, Naota discovers that his father Kamon has hired his mysterious assailant, Haruko Haruhara, to be their housekeeper and moreover, that they will be roommates. After learning from Haruko that she is "an alien" and frustrated with her, he goes downstairs and discovers that Mamimi had stopped by. Naota runs off and meets her at a bridge, where suddenly a robot, followed by a detached robot hand, emerges from the horn on his head, and begin to fight. After the robot triumphs, it is struck by Haruko with her guitar.
Opening song: One Life
Haruko’s intro: Runners High
Haruko and Naota at railroad crossing: Stalker
Manga Scene: Come Down
Naota runs to Mamimi: Bran-New Lovesong
Mamimi Overflows: Advice
Robot fight: Sleepy Head
Next morning: Little Busters