The student council president, Ayano Sugiura, shows her annoyance at always placing behind Kyōko in tests, while her assistant Chitose Ikeda fantasizes about the yuri potential between the two. Meanwhile, two classmates, Himawari Furutani and Sakurako Ōmuro, are at war with each other as they are both vying for vice-president position. Ayano later gets a cold so the others pay her a visit.

With Yui now living alone in her own apartment, she invites the others over for lunch. After Akari and Chitose leaves, Kyōko decides to spend the night only to remember she hasn't finished her homework.

The girls write Tanabata wishes, with Kyōko becoming annoyed at how Chinatsu's wish is responded to by Yui. Ayano studies fiercely to reach the top of the final exams, only to become disappointed to find Kyōko hadn't studied due to the exams conflicting with a doujin deadline. Later, everyone heads to the beach, where Ayano's attempts to be more friendly with Kyōko prove to be near fatal for Chitose's imagination.

Ayano unwittingly gets dragged along by Kyōko, Yui and Chitose to a doujinshi convention in Tokyo to help Kyōko sell her dojin. Himawari and Sakurako work on their summer homework, where Sakurako talks about why she joined the student council. Meanwhile, Akari and Chinatsu have a confusing conversation about the latter's feelings towards Yui, which leads to Chinatsu practicing "kissing" on Akari against Akari's will just as Yui and Kyōko walk in.

A visit by a first year student inspires Kyōko to draw a doujin about her and Yui, prompting Chinatsu to respond with her own story, presented in a fearsome art style. They then decide to make some clay art figures. Later, everyone meets Yui's relative's child, Mari, with Chinatsu reluctantly dressing up as her favorite anime character for her.

With Christmas coming up, Kyōko holds a lottery to arrange the girls into pretend couples for mock dates. Kyōko and Chinatsu go to the movies and the arcade, Akari and Chitose visit some cafés, Himawari and Sakurako go to a restaurant while Ayano and Yui just sit around talking about their friends. Later, the girl's spend New Year's at home where they check their greetings cards from each other.

On April's Fools Day, Chitose decides to play a lying game with Ayano, who later discovers that all of her supposed lies were actually true. Later, Kyōko tries to get the attention of Chitose, only to discover it to be her twin sister, Chizuru, who doesn't particularly take too kindly to Kyōko.

The girls try to find way to distract themselves from the Summer heat. While visiting the student council room for some cooling comfort, they meet the silent student council president, Rise Matsumoto, who they mistake for a spirit. Meanwhile, the science teacher, Nana Nishigaki, decides to do her experiments in the student council room.

Kyoko and Yui, along with Ayano and Chitose, go on a school trip to Kyoto, where they explore the town, have a bath together and engage in a pillow fight.

Akari, Kyoko and Yui reminisce their childhood days when they were being bullied by a certain pink-haired girl. Later, a bump on the head causes Kyoko to become uncharacteristically polite. The others soon begin to miss the old Kyoko, especially when Kyoko plans to disband the Amusement Club, so they decide to hit her on the head again to return her to normal.

Everyone decides to have a sleepover at the clubroom during the summer. Kyoko arranges a contest between the Amusement Club and the student council. After everyone has some barrel baths, Chitose goes on a kissing rampage as a result of eating chocolate.

Yui has a tough time getting Kyōko to concentrate on her homework. Later, the gang try and come up with nicknames for each other. Meanwhile, Sakurako attempts to catch a snake that is loose in the Student Council room. Later, the girls discuss how to prevent getting a cold, though Kyōko ends up getting a cold regardless.

Akari, Chinatsu, Sakurako and Himawari try to think of ways to pass time in class. Later, Himawari agrees to help teach Chinatsu to knit a scarf, which leaves Sakurako feeling lonely without her. As Valentine's Day comes and the girls give each other chocolates, Himawari gives Sakurako some Valentine gifts.

After Ayano becomes bothered by allergies during a high pollen season, the student council clean up their room, with Ayano having trouble keeping her special pudding away from Sakurako. Later, Nana ends up making various useless inventions when the student council just want their clock fixed. Meanwhile, the Amusement Club try to find ways to pass the time while waiting for the rain to pass.

As Kyōko realizes she needs to buy new batteries for her air conditioner, she gets distracted and ends up visiting everyone's homes, only to end up buying the wrong batteries after all. As she decides to have everyone go to the pool instead, Akari misses her train and tries to pass the time til the next one comes. Later, Kyōko visits Yui while she has a cold while Sakurako and Himawari follow Akari around.

The girls come to Comuket to help Kyōko run her doujin table, which is showing off a fan-made anime of Majokko Mirakurun in which Mirakurun fights against Team Giga Giga after they steal all the balls in the world. After selling out their stock, the girls go around in cosplay, where Chinatsu once again ruins the image of Mirakurun for young children. After Comiket, Kyōko brings up a box of conversation topics, including some weird ones.

Sakurako gets pushed around a bit by her sisters Nadeshiko and Hanako whilst Himawari's little sister Kaede is a bit too inquisitive. Meanwhile, Chizuru decides to clean up Chitose's room whilst she is out, but has to take extreme measures to stop picturing her and Ayano together and drooling all over the place. Later, Himawari worries that she's gained weight and comes to Sakurako for some exercise advice. Elsewhere, Chinatsu talks with her older sister, Tomoko, who has a crush on Akari's older sister, Akane, who, at that moment, is doing perverted things with Akari's belongings whilst she is away.

As Kyoko asks the others to help finish her doujin for a deadline, they are reluctant to let Chinatsu assist in anything artistic. Later around Christmas time, everyone goes to a karaoke place, where Chinatsu fails to get a duet with Yui. As a consolation, Yui takes Chinatsu to the movies, where Chinatsu's plan to cling onto Yui during a scary movie backfires.

As the first years try to study for their exams, Sakurako has a hard time keeping focused. Later, Chinatsu ends up inadvertently hiding from the others and can't find a good opportunity to reemerge. During a sleepover at Akari's house, Chinatsu has trouble sleeping after watching a scary movie. Later, each of the first years end up encountering one of their seniors, resulting in some curious conversations.

As the second years are going on a school trip to Kyoto which brings up all sorts of déjà vu, Sakurako decides to go on her own 'trip' with Himawari, only to wind up getting lost. Meanwhile, Akari tries to cheer up Chinatsu as she becomes depressed over missing Yui and winds up in another dangerous situation. Later, as Himawari visits Sakurako's house, Nadeshiko recalls how the two used to be much closer in their childhood.

Whilst clearing out the closet, the Amusement Club finds a time machine which accidentally sends Akari back to the day before she started middle school. Stuck in the past until she can figure out how to fix the time machine, Akari decides to try and rectify the mistakes her past self made so she'll have a bigger presence. She ends up being spotted by Akane, who remains supportive of her. After failing her attempts to rectify her embarrassing middle school debut, Akari goes to Nana to ask for help in fixing the time machine. As Akari spends the next week hiding out in Akane's room, Akane warns her that changing her past might replace her old memories. As Nana manages to fix the time machine, Akari spots one more opportunity to save the presence by delaying Ayano from interrupting her, but stops when she thinks about losing her old memories. As Akari returns to the present, she finds everyone has been worried about her since she had disappeared for a week.

Kyōko brings a bunch of old toys to the clubroom for everyone to play with. Later, the school holds a culture festival in which the Amusement Club and School Council put on a bizarre production of Snow White, with Kyōko in the lead role.

Yuru Yuri's protagonist Akaza Akari here!! Yuri Yuri has returned to TV! Since summer vacation is over and school is starting, I hope to have lots of fun with the members of the Amusement Club! Now let's head to the club room!

S-Sugiura Ayano here! No one told me it was my turn to do this! I'm glad to be back here with everyone. I-I didn't come back here for you! But thanks for waiting! Huh? My mom's calling me. What could it be...?

Tada! Omuro Sakurako-sama has arrived! Has everyone been doing well? I'm always full of energy! Come to think of it, the other day I studied with Himawari. I think Himawari's... uh... b-breasts might have gotten bigger again... Argh! She even lectured me, too. Okay, I've got a good idea!