Yui and the other girls start their third year at high school (Azusa's second). Yui, Mio, Ritsu and Tsumugi are surprised that they, along with Nodoka, have been put into the same class. It soon becomes apparent that their new homeroom teacher, none other than Sawako, had arranged it that way so she had fewer names to remember. With Azusa being the only second year of the light music club, the gang become determined to get new members so that she will not be the sole member when they graduate. However, their various attempts to attract new students fail, so they focus instead on their performance for the freshman reception. Azusa becomes depressed that no new members show up afterward, but after talking with Ui and Jun and overhearing Yui's comments, she decides it is fine with just the five of them for now.

While clearing their personal belongings out of the club room, the girls find an old guitar that used to belong to Sawako. Since it had aged a bit, Sawako allows the girls to sell it and add the money to the club's budget. After visiting a home superstore to buy a storage shelf, they take the guitar to the music store where they are surprised to find it valued at ¥500,000. When Sawako inquires about the sale, Ritsu tries lying about its value, but it backfires when Sawako asks for a receipt and the club end up getting considerably less money. However, she allows the girls to buy one thing with the money. Noticing that Azusa looks a bit concerned about not having any freshmen to look after, the girls decide to get her a pet turtle named Ton.

After noticing how badly she shows up in videos of the band's performances, Ritsu decides she does not want to be the drummer anymore as she does not stand out enough. She tries playing the guitar but cannot get beyond the basics. She tries the keyboard next, but only goes as far as playing with all the sound effects. The next day, Yui tries coming up with various ways to make Ritsu stand out, with no such luck. Later that night, Ritsu recalls when she first started drumming and practicing every day. After watching a DVD of The Who, she realizes that even though she is not always in the spotlight, she loves playing the drums. The next day, Tsumugi shows off a new song that Ritsu helped her come up with.

The third years go on a school field trip to Kyoto. On the train there, Mio is a little annoyed at Yui's and Ritsu's childish behavior. Mio realizes that she will have to watch over both of them during the trip. After visiting various shrines and attractions, the group returns to the inn where the girls' bad habits continue to annoy Mio. The next day, they have a look around Kyoto, though Mio laments that no one wants to participate in any tourist activities. However, when they get lost on the way back to the train station along with Nodoka's group, Mio gives in to the jokey nature of the others and loosens up for the rest of the trip.

Azusa and Ui, along with their classmate Jun, spend time together while the third years are on their trip to Kyoto. Noticing that Ui would be lonely without her sister around, Jun and Azusa decide to sleepover at her house, in exchange for Azusa helping out with her underclassmen in the jazz club. After spending the night, they wake up to a rainy day. They go to an arcade where Ui hits a home run in a batting game, before Azusa is reminded that she needs to feed Ton. While in the music room, the three decide to have a jam session together. The other girls return the next day and give Azusa a keychain, one of a set that spells out 'light music club'.

On a very rainy day, Yui gets completely soaked trying to keep her guitar from getting wet. While Yui lets her clothes dry, she temporarily wears a maid costume made by Sawako until she gets told off about it. Azusa later helps Yui maintain her guitar. When it continues to rain the next day, the others recommend Yui keep her guitar in the clubroom overnight, though it causes her to worry late at night. The following day, Yui is so overjoyed to be reunited with her guitar that she brings it to class, but Sawako tells her to put it away.

Mio gets the feeling that someone is watching her, making her feel uneasy, though it turns out to be because she had a sticker on her hair. She is visited by Nodoka, along with a couple of members from Mio's fan club. The girls are reminded of the previous year, where Mio felt like she was being stalked by someone and went to the student council for advice. There, she met the former student council president Megumi Sogabe, who suspiciously appeared to know a lot about her and the light music club. It was soon revealed that Megumi was not only Mio's stalker, but was also president of her fan club who had wanted to see as much of her as possible before she graduated. As a graduation gift, Mio and the girls held a private concert just for her. After Megumi graduated, she passed the position of fan club president over to Nodoka. Since she had not found time to do anything for the club, Nodoka asks the light music club to hold a special tea party for them. Mio is initially embarrassed by all the skits, interviews and service she has to put up with, but warms up when she sees a slideshow of her times with the light music club. The event ends with a performance and a group photo, which Azusa sends to Megumi.

While filling in University Choice forms, Yui and Ritsu get in trouble for not being decisive enough about their future. Nodoka tells the others about how Yui somehow became friends with her after they met in kindergarten and how she has improved since joining the light music club. Mio and Ritsu later tell how they met and how Ritsu helped Mio when she was nervous about reading her award-winning essay in front of others in fourth grade. When Yui attempts to put 'musician' as her career choice only to be rejected, Nodoka cannot help but laugh. Yui asks her classmates for some advice, but still gets confused, so she just says she will do her best for now, which is still rejected.

As the finals approach, Yui is struggling with her studies. One of Yui's neighbours, a kindly old lady who's always taken care of her, tells Yui about an upcoming talent show event taking place right after the finals. Wanting to pay her back, Yui decides to enter, though the others are concerned about her juggling two priorities. Azusa decides to join her act and help her study for the finals. After their tests, Yui and Azusa perform their routine. Though they didn't win, Yui gives her participation prize to the old lady as thanks. Yui manages to pass her test with high scores.

After Sawako gets a call on her phone from someone in the clubroom, the girls decide to follow her. There, they find her meeting up with one of her friends, and although they are easily noticed by her, she does not alert Sawako to their position. After Sawako leaves, her friend introduces herself to the others as Christy, a guitarist from the previous light music club during Sawako's punk phase, and reveals that one of their group's other members is getting married. At the wedding, Sawako is shocked to find her old death metal band on stage with Yui as the guitarist. When Yui gets off to a nervous start, Sawako sheds off her shameful pride and takes her place on stage.

During an unbearably hot day, the girls have trouble beating off the heat and also notice Ton shedding in its current aquarium tank. After dragging Sawako away from the air-conditioned staff room (partly to give Tsumugi a ride back to her house to get a bigger tank for Ton), the girls wonder why the club room does not have an air conditioner. After inquiring with Nodoka about it, it turns out that Ritsu never sent in a request for an air conditioner due to her never attending any student council club meetings. After pleading to the student council, the club room gets one installed. However, Yui slumps over, having forgotten that she weak to air conditioning.

With summer vacation starting, everyone initially decides to do another training camp, but instead they decide this year to go to a summer rock festival in the mountains, which Sawako conveniently has tickets for. After following Sawako's strict survival guide, the festival starts and everyone gets into it, especially Mio, although Tsumugi and Yui become depressed when they cannot eat the foods they want. Meanwhile, the girls shortly go separate ways to listen to different bands. While Mio gets entranced by a left-handed guitarist, Sawako enjoys headbanging to a heavy metal band far from the others. After a day of music, the girls sit under the stars, listen to the bands far away, and agree to perform at the next Summer Festival.

With the other girls studying for their exams, Azusa hangs out with Ui. Throughout the day, Azusa spaces out and has weird dreams concerning the other girls. Later, Azusa, Ui and Jun go to a swimming pool, where Jun starts to regret not joining the light music club. Afterwards, they run into Yui and the others for real and they all go to a summer festival together before Azusa, Ui and Jun lose them in a crowd. Jun mentions that she might join the light music club if they cannot get any other members by next year. At the end of the day, Azusa worries about being all alone and promises to make the upcoming school festival performance a success.

Unable to get Mio to hang out with her, Ritsu runs into Tsumugi who decides to hang out with her. They go to an arcade and then to a candy store, where Tsumugi is fascinated by all the cheap items. Meanwhile, Yui has Nodoka over to help with her homework, and gets upset when she eats the strawberry off her cake. Later, Tsumugi asks Ritsu to hit her, wanting the same skinship she has with Mio, but Ritsu cannot bring herself to do it. As a compromise, Ritsu attempts to train Tsumugi to be dopey enough that Mio would hit her instead, but to no avail. Hoping to make an opportunity, Tsumugi eats the strawberry off Mio's cake, but this just makes her cry. Having given up when a direct request to Mio also fails, Tsumugi finally gets hit when she implies Ritsu would be popular with the girls if she was a boy.

Upon returning to school after summer vacation, the girls learn of a school-wide marathon, which Yui is not keen on participating in. Seeing the marathon course while riding in Sawako's car does little to make her look forward to it. During the marathon, Yui constantly gets distracted and later everyone starts getting tired, trying to come up with various ways to keep them motivated. After reaching the top of a steep hill, the girls discover Yui has gone missing and go search for her. When Ui hears about this, she deduces that Yui had been staying at the old lady's house after scraping her knee. At the final stretch, Yui assumes that there will not be a rice cake for the person in last place, causing everyone to make a dash for the ending, resulting in Mio, who did not want to finish last due to it being embarrassing, performing an extravagant roll upon tripping at the finish line. While everyone enjoys red bean soup and rice cakes, Sawako is still searching for Yui.

When Azusa comes to the realisation that the light music club has been slacking as of late, she becomes determined to practice more. Azusa runs into Tsumugi alone in the club room and tries giving her some guitar lessons. She later is about to get a chance to practice alone with Mio, but is interrupted when Ritsu requires help from Mio and the girls end up spending the evening at Ritsu's house. The next day, Azusa runs into Yui in the club room hoping to practice, but ends up cleaning Ton's tank and helping her with understanding how to play the song Tsumugi composed, as she cannot read sheet music. Yui reminds Azusa that she is who she is, and personalizes her keychain.

The club room is closed for repairs, leaving the girls nowhere for practice. While trying to find a suitable location for their practicing, the girls try to come up with lyrics for the song Tsumugi wrote. Failing to find anywhere in the school to practice, they rent out a studio, but end up wasting time discussing lyrics and run out of time before they can practice, though the club room reopens the next day. The following night, Ui helps Yui write some lyrics, but ends up catching a cold, leaving Yui, who has always relied on her, to look after her instead. Realizing how important she is to her, Yui writes some lyrics dedicated to Ui, which are approved by the other club members.

Much to their dismay, Mio and Ritsu are respectively nominated for the roles of Romeo and Juliet in the class play. Mio has her usual problems with the pressure of being centre stage, whilst Ritsu can't act lady-like enough for her role. After not being impressed with the other girls' 'training' for them, Ritsu and Mio decide to have a cram session. Whilst doing impersonations of each other if they switched roles, they find the key to successfully acting out their parts. Noticing Mio still lacks confidence, Tsumugi arranges for her and the others to work as maids in her family's tea shop to help get over her embarrassment. Although she gains some confidence, Mio still is reluctant about being centre stage. Meanwhile, Azusa grows concerned that, with everyone rehearsing for the play, no one's preparing for the live concert.

As the seniors prepare for the play, Azusa worries that there has not been enough practice for the live performance. As the play goes on, the backstage crew realize they are missing Juliet's gravestone needed for the climax, but manage to borrow something from the occult club in time. After a successful play, the girls apologize to Azusa for making her worry and decide to hold an overnight practice session at school. Later that night, they browse through the closed stalls, where they find the missing gravestone, and give their thanks to the occult club. The next morning, Sawako gives the girls special Ho-kago Tea Time t-shirts for their performance.

The girls get on stage for their performance and are surprised to find everyone in the audience wearing the same shirts as they are, which moves Yui a lot. During their performance, they sing two new songs, and Yui gives her thanks to the people who have helped her, and even gets thanks in return from the others. After their performance, the girls look back on their previous years and start to become upset knowing that this is their last year together, but manage to cheer each other up.

With photos for the graduation yearbook coming up, Yui uses Ui as a model to determine the best hairstyle, though feels weird when she leaves her hairpin on her. Although the seniors have finished their clubs, the girls decide to use the music room to study for their entrance exams, though Yui and Ritsu still have yet to decide on their university choices. While trying to trim her bangs for her yearbook photo, Yui sneezes and accidentally cuts them off, giving her a completely different look. After their pictures are taken, the girls learn Mio had turned down a recommendation for a university because she wanted to study together with everyone. Upon hearing this, Yui, Ritsu and Mio turn in their university preference applications to Sawako, opting to go to the same women's university as Tsumugi.

As the seniors prepare for their entrance exams, Azusa decides to make them a chocolate cake for Valentine's Day, getting Ui and Jun to help. When the day comes, Azusa becomes nervous about presenting the cake to them, also worried about their impending graduation. However, her friends encourage her and the cake is well received, even getting a speedy White Day gift from Yui. The next day, Azusa makes an expensive prayer at the shrine for the girls' success, and later receives word that they have all passed their entrance exams.

Although they are not supposed to be at school until graduation the next day, Yui and the others decide to hang around the club room, though they have trouble figuring out how to pass the time. They clear out their desks and visit the student council room before getting Azusa to buy them some lunch. Wanting to leave something behind after they graduate, the girls decide to record an album of their songs.

On the day of the girls' graduation, Yui gets off to a rough start by being late and ripping her tights. Meanwhile, Azusa is similarly distracted and ends up banging her head. The girls hold onto something, though Yui's attempts to hide it during the graduation ceremony cause Sawako to grow suspicious. They later give Sawako the present, a card signed by the entire class, later that day as thanks for being their teacher. After the classroom empties, leaving behind several goodbye messages for Sawako, the girls go to the light music room, shortly followed by Azusa. Azusa, who had been holding in her feelings all day, finally breaks down into tears, begging them not to graduate. To cheer her up, the girls perform a special song they wrote just for her.