Kafuka Fuura is cheerily walking to school one April morning when she suddenly spots a man trying to hang himself in a fit of despair. Kafuka manages to use her weight to snap the rope, thus saving his life. Nozomu Itoshiki, the man, eventually cannot take anymore of the girl's ridiculous ramblings, and runs off to school to start homeroom at the beginning of a new school year. When Nozomu walks in the door, he finds Kafuka is one of his students.

After confiding in his latest despairs to Ms. Arai, she asks Nozomu to visit one of his students who hasn't shown up to school — Kiri Komori, a hikikomori. In the end Kiri goes to school but decides to be a hikimori there. The next day, Nozomu notes that another of his students, Matoi Tsunetsuki, didn't show up that day. Ms. Arai brings Nozomu to the counseling room, where she explains Matoi's obsessive-stalker tendencies to Nozomu. That night, he attempts to dissuade her from bothering her last boyfriend; however, his strategy backfires on him. This turns him into Matoi's latest object of affection.

This episode is a pastiche of parodies about foreigners and Japanese attitudes concerning them. A foreign student named Kaere Kimura transfers into the class. Kimura is a blonde girl with multiple personality disorder stemming from cultural identity confusion. Nozumu prevents her from committing suicide but sees her underwear and is sued. While Nozomu is absent from school Chiri investigates his students and discovers that Maria is an illegal immigrant.

Chie dispatches Nozomu to investigate rumors that the invariably injured Abiru Kobushi is suffering from domestic violence. He pursues Abiru's father while he shops, causing him a great deal of inconvenience, before discovering Abiru's obsession with pulling the tails of dangerous animals. The latter half of the episode concerns Meru Otonashi, who is silent and shy in person, but remarkably abusive via text-messaging, her only means of communication.

On physical examination day, many of the girls are feeling stress about their weight, measurements and fitness. Nozumu distracts them by deciding to judge the "social worth" of students so that they will know whether they are living "above their station." Kitsu seizes on this idea, scolding everyone who possesses any luxuries, appalling Nozumu to the point where he decides to go on a hedonistic binge before killing himself. In the second half he encounters some of his students at a hot spring and is frightened to learn the spring has the power to remove their "toxicity" giving them well-adjusted personalities.

Kafuka comes down with a cold during the summer and has to go see the doctor, Mikoto Itoshiki, who happens to be Nozomu's brother. Later, Chiri and Kafuka find out from Mikoto that Nozomu has gone back to his hometown in Kuraizawa for an arranged marriage. One way or another, the girls somehow all end up arriving at Kuraizawa, where they are taken to the Itoshiki residence by Tokita. Here they find out that the Itoshiki tradition for arranged marriages simply involves both parties exchanging eye contact. The rest of the episode involves Nozomu and his attempts to avoid eye contact with the girls and various other people/objects.

This episode begins with Fujiyoshi bumping into Nozomu while she is on her way to make copies of her doujinshi. Through a misunderstanding, Nozomu ends up going to Comiket to sell his doujin literature with mixed results. At Comiket, Chiri reads Fujiyoshi's yaoi doujinshi. On the way back from Comiket, they meet Kafuka, who talks Chiri and Fujiyoshi into drawing more manga that strictly adheres to the above mentioned format. The second half of the episode involves the girls at a matsuri, where overzealous festival-goers begin piling random objects and people on portable shrines and dancing and parading around with them.

This episode begins with Usui Kagerou lamenting about how he never gets noticed by anyone, when he nearly gets run over by a truck who does not notice him. He runs into Nozomu in the shadows, who begins to talk about how some people are destined to be overshadowed by others, no matter how hard they work. The second part of the episode has the class undergo criticism training. Usui continues to be ignored until a divine wind blows away his hair, revealing his bald head and allowing everyone in the class to see him. He fears that people in the class will begin mocking him, but Kafuka suggests that Chie insults him instead, which he seems to enjoy.

Nozomu notices a few members of the class playing a "spot the differences" game. Nozomu tells them that it is important to spot mistakes and he instructs the class in how life is filled with mistakes. He asks the class to identify mistakes in their lives after pointing out several of his own. After Nozomu contradicts himself, saying that a mistake was the correct action, Kafuka reasons that if a mistake comes to light, it is correct, resulting in many people approaching her, confessing their mistakes, making them correct. In the end of the first part, a boy approaches Nozomu, calling him "Dad." The second part of the episode reveals that he is actually Nozomu's brother's child, Majiru. Nozomu asks him to prove that he is indeed his nephew, and then asks all of his students to prove that they are the real one. When Majiru asks Nozomu to prove he is genuine, Nozomu is unable to come up with a response, and runs off. The episode ends with a sequence that deals with Majiru's hair fetish.

The episode begins with Nozomu announcing there will be a cultural festival, which he decides to not participate and explains that they are not cultured people, believing that they will grow to be bad people if they do pretend they are. The second part of the episode starts with the class taking a field trip preview, where Chiri make a large itinerary guide of the place. They move quickly all over Kyoto until they come to a temple. There the monk enlightens them about the use of preview. The episode ends with Nozomu take Chiri to visit his preview funeral and gravesite, where she gets angry and hits him, sending him to the hospital and putting him in a coma (which Kafuka calls a "preview of the afterlife").

The first part of this episode introduces Ai Kaga, a girl who always takes blame for everything, even though it is not her fault. Nozomu takes the class to a "guilt scramble" to explain that history has led to the "guilt complex" such as Kaga's becoming the Japanese mentality. After being overcome with guilt himself, Nozomu and Kaga travel the world to try to stop burdening others. The second part introduces another girl, Mayo Mitama. Her evil-looking eyes have led to her being misunderstood - that is, she actually is evil, but people try not to prejudge her and assume she is actually good. She commits several cruel acts that Nozomu bears witness to and is blamed for, being the only other nearby party. He becomes so concerned with not prejudging that he doesn't blame her when she hits Majiru over the head with an aluminum bat or when she drops a brick onto Nozomu's head.