Mr. Kubodera made his first appearance in "Rough Sketch", introducing the new transfer student to the rest of the class, clarifying that if everyone supported each other and worked together, they could "get through the year in good shape". After that, he dedicated himself to his job as a teacher of the course, teaching mainly writing and literature.
Then, after the death of a student and a family member of another, Mr. Kubodera kept his class lively, repeating that if everyone stayed together, they could finish the year. In "Build Limbs", after Kōichi was questioned about Sanae Mizuno's death, Mr. Kubodera appears by the door to ask him if he had finished the interrogation, and then indicate to Kōichi that he could go home for the rest of the day, he also clarified that the new female representative of the class had been chosen, but not before reminding her to try to follow "the rules of the class".
Later, lamenting over the death of Ikuo Takabayashi, Mr. Kubodera instructs his class to stay together and not feel bad for all the terrible events that happened, reminding everyone to follow the rules of the class, and only then can they overcome it. He also says that Ms. Mikami has been supportive despite feeling quite bad because of the constant incidents.
In "Face to Face", in a flashback, Mr. Kubodera explains to Mei Misaki her role as "the one that does not exist" and that she has the right to refuse, but that in case she does it while the calamity begins... She also says that it was better to keep it only with Class 3-3 students and teachers, not including teachers from other classes or family members. Then he appears in Kōichi's dream with Mei, and later, even knowing that two students had been absent, he is seen teaching a class that later would become "his last class". The next day, he presents himself to the class with a large bag which he hits with the podium to indicate to the class about his presence, during his talk he explains to the class about his attempt to make the class pass the school year, telling that from that moment on, all that happened would be problems that they themselves had to face on their own, and that they had tried to do everything possible to prevent this from happening, saying that it was "useless to talk about this now"; he then took a large kitchen knife out of the bag.
At the beginning in "Sphere Joint", Mr. Kubodera takes the knife and holds it to his neck while screaming and waving the knife in the air, only to end up stabbing himself in the neck, after which he spits out a bloodstain that falls on Sachiko Nakajima, in all the pain and brutality of the event proceeds to stab himself deeper to end up spraying his entire class with his own blood and collapses onto the ground. After this horrific event, the entire class leaves the classroom horrified and screaming, except for Kōichi and Mei, who observe the corpse, and a few other students who went into shock. Mei tells Kōichi that apparently making two non-existent students was "totally useless".
Then, it is shown a moment before the suicide where Mr. Kubodera walks with Tatsuji Chibiki, explaining to him his fatigue and his doubts about what he should do, only to be shown walking to school with his bag. Mr. Chibiki then mentions that the police decided to invest in his house, where they found a rather disturbing event, which was the body of Kubodera's mother Tokue, who had apparently been murdered; Later it was believed that the class problems and calamity weighed heavily on Mr. Kubodera's mind, and that without any other remedy he had decided to murder his mother and then take his own life in front of his entire class.
Finally, in "Body Paint", he appears in Kōichi's nightmare with the other victims, with the knife to the neck and blaming Kōichi for everything that happened.