Kyosuke confronts Hiro about what happened with Kei, telling him that he always does things halfway. Miyako calls Hiro to tell him that it is too painful to be with him since she does not want to be eventually forgotten by him. Hiro goes to see Kei and is able to come to an understanding with her, even though he is in love with Miyako. Right before she is going to leave town, Miyako calls Hiro one last time. The calls cuts out at a pivotal moment, which leads Hiro to rush out on his bike, managing to find her at a public public telephone booth near a church where they kiss.

Hiro finds Miyako at a public telephone booth in town and after a stroll on the beach where they kiss, Hiro takes her back to his place where they make love. The following morning, Kei finds Miyako in Hiro’s bed, which causes her to run away in tears, eventually collapsing on the road as Kyosuke rushes up to her with his bike. Renji continues to stay with Chihiro despite the pain he feels and manages to smile when around her. Chihiro rereads her diary three times and eventually comes to act like the person described in her diary, but she thinks that person is already dead. After hearing this, Renji vents his frustration and continuously repeats that this is not true.

Frustrated that none of her voice messages made it through to Hiro, Miyako tossed her cell phone into a nearby fountain the night he stood her up. Hiro tries to call her repeatedly, but could not get through due to this. Miyako later calls him on a public phone and is reassured that Kei lied to her when she said Miyako had already disappeared from Hiro’s heart. Renji and Chihiro continue work on the novel, and Chihiro is pushing herself with stress and lack of sleep so as to prolong her memories. She eventually collapses and is unconscious for over thirteen hours. When she finally awakes, Renji witnesses Chihiro’s frantic state of not understanding why she has grown older or what happened to her left eye.

Renji and Chihiro continue work on the novel at his school’s library and they manage to nearly complete it. Afterwards, the two take a walk on the beach and Chihiro suddenly asks Renji if he wants to kiss her. This seemingly simple act throws Renji off balance and says that their relationship is not like that, which causes her to run away in tears. Renji breaks down, hoping she will not write down what just happened in her diary. The story shifts to a flashback of when Miyako was waiting for Hiro to show up for their date in the previous episode. Miyako continues to send him voice messages on his cell phone, first being angry for him not showing up, but later becoming increasingly desperate with each call as she does not want Hiro to ignore her. The story shifts back to the present in Hiro’s room, with Hiro and Kei together. After Hiro leaves his room to get food, Kei discovers Miyako’s messages before Hiro learns of their existence, and promptly deletes them, as she vowed to erase her from his memories.

It turns out that Kyosuke asking Kei out was a ploy on his part as a lead in to ask her if she wanted to star in an amateur film he is making for an upcoming film festival. Hiro and Kyosuke get into an argument over the differences between being a professional and an amateur, however Kei interjects in her indecision on whether or not to be cast in Kyosuke’s film. Later, Kei informs Miyako in an intense discussion that Miyako will eventually disappear from Hiro’s heart. On Sunday, Kei gets hurt at the basketball match, and Hiro ignores his date with Miyako in order to make sure Kei was all right. Meanwhile, Chihiro continues to write her novel, and Renji helps her by borrowing a uniform from Kuze so that they can enter the school’s library to research materials for the novel.

Renji brings Chihiro to his home where she meets his mother Sumire Aso and his neighbor Shuichi Kuze, though she has merely forgotten the latter many times over. After they eat, Chihiro gives Renji a notebook with her notes for her novel which he reads after she leaves for the day. He finds that the novel is rather depressing and representative of Chihiro’s life. At school, Kei tries to get Miyako to leave Hiro alone so he will not have to repeat a year of school, but Miyako talks down to her the entire time. Kyosuke films Kei in the morning while she is taking a basketball shot, and she punches him in the gut for filming her without permission. He later asks her to go out with him via Hiro’s help.

Renji sees Chihiro for the first time after she gets over her cold and apologizes for not coming last time. Renji asks her if she would like to write a novel with him, as she had said earlier that it was her dream to write one, but Chihiro gets very defensive and angry at his request. After talking with her more on the issue, Chihiro finally gives in to his persistence. Kyosuke sees Kei again in town and finally realizes she was the one he filmed on Christmas. Hiro meets with Miyako in town and she goes back to his place while he works on his manga. Miyako reads some of Hiro’s manga, and as an act to show her gratitude, she cooks food for him. Kei walks in on them together, and runs off.

Renji continues to meet with Chihiro every day after school, though he wonders if he should continue with such a half-hearted attitude. It rains one day after school, so Renji does not go to meet Chihiro, thinking that she would not come under the circumstances, but she comes anyway and manages to catch a cold, something Renji feels terrible about later on. Hiro goes out during school with Miyako into town and they have lunch at a café. After Hiro accidentally forgets her given name, Miyako leaves him behind at the café. Kyosuke quits the film club, and even breaks up with his girlfriend.

Chihiro tells Yuko and Kei about Renji. Kei wakes Hiro and forces him to get up and go to school. While ditching classes, Hiro runs into Miyako again, and finds out that they are in the same year at the same school, though in different classes. He tells her that the reason why he does not attend classes much is that he is already an established manga author. Kyosuke continues to ponder over the brief shot he got of Kei running through the city on Christmas, though he does not recognize her. Renji meets again with Chihiro and becomes closer with her. He eventually finds out from her that she has a memory defect where she cannot remember anything past thirteen hours previous.

Renji Aso meets Chihiro Shindo at an abandoned train station one day after school, and returns to the same station several days in a row to see her again, finally declaring friendship with her on the third day. Kyosuke Tsutsumi is out with his girlfriend on Christmas night when he is distracted by Kei Shindo running down the street, but a passing truck spoils his shot. On his way to Kei’s Christmas party, Hiro Hirono stops at a church to do research, where he is surprised to see Yuko Amamiya, then Miyako Miyamura rides off on his bike in pursuit of a purse snatcher. In the same church, Renji asks Yu Himura for career advice and is told to follow his passion. Miyako winds up spending the night with Hiro after crashing his bike and knocking herself out, and Hiro never makes it to Kei’s party.

“School Days” “Sukūru Deizu” (スクールデイズ)

Sekai disappears, and Makoto is wandering around aimlessly until he meets up with Kotonoha again, under the town’s Christmas tree. As they pass the night together and Sekai witnesses the two of them heading back to Makoto’s place. Just to make sure her eyes weren’t playing tricks on her, Sekai heads over to his place…

“To Be Announced” “Mitei” (未定)

Konata and her friends prepare for the school’s cultural festival. Patricia decides to have the girls do a cheerleading session set to the show’s theme song, which hassles the girls between preparations for their class’ cultural displays and preparations for the routine. At first, Patricia has a hard time trying to convince her friends, but then she bribes Konata with a ticket to an Aya Hirano event, where people could shake hands with her. Konata gets her friends to help out, and even though Kagami is initially against it, she becomes the most enthusiastic of the bunch to do the routine. Akira Kogami has been invited to the school as a special guest, but she and Minoru still despise each other. At the end of the day, Konata, Tsukasa, Kagami, Miyuki, Ayano, and Misao reflect on their last cultural festival. The next day, at the opening of the festival, the girls get ready emotionally for the dance, and as the curtain rises, the screen fades to white.

“Everyone’s Makoto” “Minna no Makoto” (みんなの誠)

Christmas is coming around the corner, and although Makoto is dating Sekai, it seems as if he wants out of it. So it appears as if he is haphazardly getting himself involved in other relationships, despite his promise to Setsuna. Now things are going terribly wrong, as Kotonoha loses herself, Sekai finds out about Makoto’s infidelity, Setsuna’s move to France and most importantly a sudden change to her body…

“Delicate Line” “Bimyō na Rain” (微妙なライン)

Konata and Yutaka get sick at the same time, but while Yutaka can only rest in bed, Konata plays video games and is mainly using her sickness as an excuse to get out of class. When Minami, Patricia, and Hiyori come to visit Yutaka, Yui reveals that Yutaka has been talking about Minami a lot, but Yui reveals nothing about Yutaka saying anything about either Patricia or Hiyori. After Miyuki hears about gum that will help prevent cavities, she tries a piece, but inadvertently causes an old cavity filling to fall out, resulting her in having to go back to dentist’s office. Later, Minami gets embarrassed when Miyuki recounts how Konata and her friends compliment her, and then further embarrassed when Miyuki’s mother tells of a recent time when she saw Minami at the grocery store.

“Mind and Body” “Kokoro to Karada” (心と体)

As the school festival comes to an end and Makoto and Sekai dance at the bonfire, it finally seems like they’re happy together and things have settled down. However, Kotonoha watches from the shadows, and obstiantly denies what has happened still believing that their still going out. Meanwhile, as Setsuna prepares to move to France she is doing some final preparations to ensure that her best friend - Sekai - will be taken care of…

“The Yonder Here” “Koko ni Aru Kanata” (ここにある彼方)

Konata’s late mother, Kanata, appears as a spirit. As she looks over her family in the room, both Konata and Sōjirō discuss what her life was like, while she was still alive. Although Sōjirō rushed Kanata into love and marriage, Sōjirō was confident that he loved Kanata the most and that she loved him back. A long flashback scene then takes place, where Kanata thinks back on all the happy times she shared with Sōjirō, and concludes that she did love him deeply as well (although she is disturbed about him exposing Konata to eroge). As Konata and Sōjirō prepare to take a picture, Kanata joins in with them, but appears as a shadow in the actual picture. Konata and Sōjirō review the picture and are highly shocked and disturbed at the shadow, and fear that they are cursed.

“After Evening Festival” “Kōyasai” (後夜祭)

Makoto makes a promise to Sekai to dance with her during the School Festival’s folkdance; however, he also made the same promise to Kotonoha. As Kotonoha mans the front desk at her class’ school festival activity, she ferverously texts Makoto and awaits for a single response back…

“Pandora’s Box” “Pandora no Hako” (パンドラの箱)

The third-years go on a trip to Kyoto. Tsukasa feeds deer, however, she eventually gets trampled by them. Kagami receives a letter from a boy asking her to come out at night; she thinks it is a love letter, thus thinks about it all day, not even saying stuff against Konata’s childish jokes. However, it turns out that the boy called Kagami in order to get a doll that he was too embarrassed to buy. The next day, Konata leads the girls on a side trip to the offices of Kyoto Animation.

“School Festival” “Gakusai” (学祭)

Makoto hasn’t told Kotonoha yet of his relationship with Sekai. However, one night Kotonoha bumps into Sekai outside of Makoto’s apartment and an altercation goes down. And with that, begins the the school festival…

“Ways to Spend Summer” “Natsu no Sugoshikata” (夏の過ごし方)

Kagami and Konata talk about collectible figures, the negative portrayal of Akihabara in the media and the relationships between otaku. Konata is reluctant to do any homework and is caught playing games and reading manga, instead of working several times by Yui. Konata, Miyuki, Tsukasa and Kagami get together to study during the summer and decide to go to a fireworks festival near Miyuki’s house. Yutaka, Minami, Hiyori and Patricia decide to go to the same festival and discover that Minami and Miyuki live across the street from each other.