Naota Nandaba's boring, ordinary life in the town of Mabase is violently interrupted when a manic, pink-haired woman named Haruko Haruhara runs him over with a Vespa and hits him in the head with a bass guitar, causing a giant robot to sprout from his forehead.
Mamimi, Naota's troubled ex-girlfriend (who was actually dating his brother), becomes obsessed with the robot Canti, treating him like a god. Meanwhile, a string of mysterious fires plagues the town, and something terrifying is gestating inside Naota's head.
Eri Ninamori, the cynical class president and daughter of the town's mayor, tries to navigate her parents' scandalous divorce. She ends up crashing at Naota's house just as her repressed emotions manifest as a mechanical menace from her own head.
Naota's father and grandfather become obsessed with baseball, but Naota refuses to swing the bat, afraid of striking out. When a massive, city-destroying satellite hurtles toward Mabase, Haruko forces Naota to step up to the plate with his guitar.
Naota gets a taste of power and starts carrying real firearms in a desperate bid to act like an adult. A massive, heavily armed Medical Mechanica robot attacks the town, forcing Haruko and Canti into a brutal, beautifully animated firefight.
The town of Mabase begins to literally flatten as Medical Mechanica makes its final move. Haruko's true motivations regarding the space pirate Atomsk are revealed, forcing Naota to finally stop acting like a kid and make a choice that will change everything.