Teenager Kazuki Miyaichi has always felt unloved by her mother due the circumstances surrounding her birth. Because she harbors anxiety and perceives herself as being worthless to others, she engages in acts of juvenile delinquency. One day, a transfer student from Yokohama named Eri introduces her to Hiroshi Haruyama, a reckless youth who’s a member of the “Nights” motorcycle gang. Kazuki finds herself increasingly drawn to Hiroshi over time, but he soon becomes leader of the Nights and gets caught up in a conflict with a rival gang.

Story continues with the students' own conflicts, Koro Sensei’s identity and the fate of the world. The time limit for assassination is approaching.