Keiji Takeda is waiting for his girlfriend, Touka Miyashita, a junior at the same school. When she does not show up at the appointed time, does not get in touch and the sun starts setting, he gives up and starts walking home. On his way, he sees a peculiar man, and like the rest of the crowd now gathering decides to not get involved. But then, a figure draped in a large cloak and wearing a strange hat rushes to the man's aid. This new figure looks exactly like his missing girlfriend.

One day after school, Kinoshita Kyouko asks Suema Kazuko to walk home with her. As they're walking along the river going home, Kyouko asks Kazuko if she knows another way home. Kazuko teases her, asking her if she thinks someone's going to kill her. Kyouko stays silent and Kazuko tells her she's overthinking things, when suddenly Kirima Nagi appears before them. Nagi then pins Kyouko to the ground.

Tanaka Shiro is worried about Kamikishiro Naoko because she disappeared, so he went to ask Niitoki Kei from the disciplinary committee for help. Kei just figured Naoko was skipping again, but Tanaka tells her that Naoko had her reasons for not showing up to school. Saotome Masami happens to hear them talking and tells them that they should talk to Kirima Nagi. Naoko and Nagi are good friends and she might know something. The three of them then go to look for Nagi.

Asukai Jin teaches at a prep school and also acts as a guidance counselor to the students at that school - but he was also born with a strange power. He was able to see what other people were missing in their hearts. He could see plants within their hearts. Everyone had something missing from their plants, such as leaves or roots. However, he couldn't do anything about what was missing in their hearts, so he tried to help them by telling them what they needed to hear. One day as he's walking home, he encounters a woman named Minahoshi Suiko, who calls herself the ...

In order to go to high school in Japan, Kirima Nagi's half brother, Taniguchi Masaki, returns to Japan. Masaki gets advice from his sister to not stand out as much at school, but ends up gathering some grudges from some of the kids at school. He gets surrounded by some students and a girl calls out to them. Orihata Aya seems to be offering herself up in Masaki's place. Because of this encounter, the two of them start to get closer, but...