Totsuko is a high school student with the ability to see the 'colors' of others. Colors of bliss, excitement, and serenity, plus a color she treasures as her favorite. Kimi, a classmate at her school, gives off the most beautiful color of all. Although she doesn't play an instrument, Totsuko forms a band with Kimi and Rui, a quiet music enthusiast they meet at a used bookstore in a far corner of town. As they practice at an old church on a remote island, music brings them together, forming friendships and stirring affections.

Yoshida, a former parliamentarian's secretary, took the fall for a murder in place of the trusted politician and ended up in prison. He awaited the day when the said politician would prove his innocence and get him released from prison. One day, while sharing a four-person cell, Machida was sent to solitary confinement for losing his temper. There were rumors within the prison that those sent to solitary confinement for punishment would mysteriously die and never return. However, Machida came back unharmed. Yet, the rumors continued, stating that returning from solitary confinement without a mysterious death was the real issue.

In the spring of a new semester, a "ranking" is sent to Class 2-D. It clearly shows the rankings of all the students and the homeroom teacher. The one who ranks 1st is Himeyama Tsubaki, a kind and popular honor student recognized by everyone. But one day, without any warning, she commits suicide. A few days later, everyone in the class receives a suicide note from Himeyama, and from that day on, the class begins to fall apart.