In 1972, a very popular honor student named Misaki died partway through the school year in Yomiyama Middle School’s class 3-3. His peers, devastated by the unexpected loss, decided to carry on as if the student were still alive, going so far as to keep his desk in place and bringing it to the graduation ceremony. Yet, no one could explain why the dead classmate was present in the graduation photo.
In spring 1998, 15-year-old student Kōichi Sakakibara arrives from Tokyo in Yomiyama to stay with his grandparents while his father works in India. He transfers into class 3-3 but misses the first few weeks as a pneumothorax keeps him hospitalized. While in the hospital, he receives a visit from his classmates and meets a mysterious girl wearing his school’s uniform called Mei Misaki, who seems to be visiting the morgue.
Once recovered, Kōichi goes to school and tries to adapt. His aunt, a teacher at Yomiyama North, gives him a few pointers but, like his peers, remains evasive when it comes to their behavior towards Mei, who is treated by all as if she did not exist. Kōichi is further confounded by the air of mystery around class 3-3 and the fact that it is isolated from other classes, even practicing P.E. separately.
Things go from bad to worse when a classmate, Yukari Sakuragi, slips while running down the stairs and dies, impaled on the sharp end of her umbrella. This is one of many deaths related to Class 3-3 which have Kōichi and his friends Mei, Naoya Teshigawara, Tomohiko Kazami, and Yūya Mochizuki, trying to unravel the mystery of 1972’s Misaki and the "calamity" that has struck Class 3-3 ever since.