Following the loss of their first baseball game, the Little Busters have a pancake party. While returning from the party, Yuiko overhears some girls badmouthing her, claiming that they will pay her back for being humiliated in the past.

After waking up, Riki learns from Yuiko that she was taking care of him while he was asleep and cannot shake the suspicion that the whole situation has happened with them in the past. Some time later, Kyousuke and the other boys point out that Riki is behaving strangely since his last encounter with Yuiko.

The day of June 20 keeps repeating without anyone taking heed of it, except for Riki himself, and no one else seems to find it strange even when it starts snowing. Riki decides to look for Kyousuke to ask for his advice but he is nowhere to be found.

While thinking about what Yuiko said to him, Riki is approached by a girl who confesses her feelings for him, but claims that she knows he already likes someone else and flees. Wondering what she meant, Rin's image come to Riki's mind.

Members of the Prefectural Assembly are expected to make an inspection of the school and realizing that it is part of the "final task" Riki and Rin volunteer themselves to guide them around. Despite Rin's shy demeanor, she manages to guide the visitors properly and they later invite her to take part in a student exchange program to help the students of another school overcome a tragedy that claimed the lives of some of their classmates.

After Riki and the others watch Rin leave the school without a word, Riki is then left with the impression that Kyousuke sent her away and that he is trying to break apart the Little Busters. Riki continues getting text messages from Rin saying that she does not know what to do at the school, and he all he can do is tell her to 'hang in there'.

Riki awakens several months before, with no memories about what happened during that time. Riki goes to stop Masato from fighting Kengo, but neither of them listen to him and Kyousuke is nowhere to be found.

Determined to reform the Little Busters, Riki attempts to invite Masato, who refuses, claiming that what only matters to him is to 'become the strongest'. Soon after, Riki and Rin hear news of Masato attacking other students and devise a trap to stop him.

Riki's next step to reassemble his friends is to convince Kengo to join their side, but Kengo refuses to listen to him, claiming that all Riki and Rin need to do is to rely on their friends. Riki visits Kyousuke, who hints that Kengo is lying about something and Riki realizes that Kengo's arm is not injured as he claims.

Having assembled the rest of the original Little Busters, Riki intends to save Kyousuke from despair the same way he did for him when his parents died. Meanwhile, Kyousuke reminisces that in fact the world they are living in hides too many things that can change the course of Riki and Rin's lifes.

After having the Little Busters once again reunited, Riki suggests for them to play baseball, and the others accept. During the match, Kyousuke reveals to Riki all the truth about the world they're currently living in.

Riki and Rin awaken in the real world and recall that during their field trip, their bus got into an accident and Masato and Kengo used their own bodies to protect them. Despite being injured, they flee from the site of the accident to avoid being caught in the impending explosion, but after reaching a safe distance, Riki leaves Rin behind to return and attempt to help the others. However, he starts suffering another attack of narcolepsy and struggles to keep himself awake.

Having another attack of narcolepsy, Riki realizes that he always falls asleep at the sight of unpleasant situations, since he saw his parents' dead bodies in a car accident when he was a child, and determined to overcome this weakness, he awakens with Rin's help. Knowing that the bus will explode, Riki and Rin start rescuing the other students from the wreckage only to discover that Kyousuke is using his own body to prevent the gas from leaking further.

The leader of the "Little Busters," Kyousuke, returns to school after a job hunting break and calls the old gang together. He suggests that they all do something that they can only do now, while they're young - and that something is playing baseball. Now all Kyousuke, Riki, Masato, Kengo, and Rin need to do is find enough new members to make a complete baseball team...

Riki meets the cheerful, easygoing Komari on a visit to the school rooftop, and decides to invite her to join the Little Busters. Meanwhile, one of the cats Rin is taking care of strolls along with a mysterious note tied to its tail...

Riki is called out for tea and a chat by Kurugaya Yuiko, a mysterious girl who rarely shows up to class. He invites her to join the Little Busters, but when she meets the team's resident musclebrain, Masato, sparks instantly fly.

On the school roof, Riki catches Komari whispering something about an older brother in her sleep. But when she wakes up, she tells him that she's an only child and her brother only appears to her in dreams, where he reads her a sad story from a picture book only to fade away when she awakens...

When Komari's normally cheerful smiles begin to look sad and lonely, Riki decides to cheer her up by searching for her older brother... but does he really exist? The next day, the two of them pay a visit to Komari's hometown in hopes of recovering her lost memories.

Komari has finally recovered her memories of her older brother - and it has left her in a tragic state of confusion. With the support of the Little Busters, Riki sets out to bring Komari's cheerful smile back.

The Little Busters are still short a few members, so Riki decides to invite a girl from a neighboring class, Saigusa Haruka, to the team. But the energetic, playful Haruka has a reputation for being the school's biggest troublemaker, and is under constant pursuit by the school's Disciplinary Committee.

When Riki sees Kud playing Frisbee with her dogs, he knows that her quick, agile movements would make her a good candidate for the Little Busters and extends the invitation. But Kud hasn't had an easy time making friends since she came to Japan, and she could use the help of her new teammates to find a willing dorm roommate.

One of Rin's cats brings her yet another mysterious note. This time its cryptic demand is to "save the school cafeteria" - but none of the Little Busters can see what about the cafeteria needs saving.

While searching for a stray ball sent flying at a Little Busters practice, Riki encounters Mio, a girl who always sits and reads in the shade of a tree with a parasol open. There's one book she's particularly fond of, but she won't tell Riki what it's about. When she loses the book, it's up to Riki to help her find it.

Kyousuke gathers the Little Busters together for a little test of courage. Their mission takes them on a search through the school building while avoiding traps set by Kyousuke, but eventually they sense that an eerie black shadow has been watching their progress...

Riki has invited Mio to be the manager of the Little Busters, and the team welcomes her warmly. However, just when they think she's finally opening up to them, she disappears...

Mio has been absent from school for several days, and everyone, even the Little Busters, seems to be gradually forgetting about her. Riki finally spots her in the courtyard again, but he notices an unfamiliar loneliness in her eyes...

When was the last time anyone saw Mio reading a book under the tree in the courtyard? What kind of person was she? Riki's memories become vague and he becomes scared that he might forget her completely. Will he be able to find the real Mio before she completely disappears?

Rin has called Riki to her room under false pretenses. Now he is stuck for the night while his friends mount a rescue attempt.

Saigusa Haruka is considered the biggest rule violator at school and the school Disciplinary Committee has it out for her, in particular Futaki Kanata. When Haruka’s family history is posted over the school the Little Busters must search for her.

The secret of the Saigusa family is explained to the Little Buster crew, and Riki wants to help his friend cope with her new Infamy.

With the encouragement of her friends, Haruka confronts Futaki and lays it all out. What Futaki has to share will change how the Little Busters view her.

Kud might be smart be she lacks some common sense concepts due to her traveling. With the upcoming practical exams the Little Busters aim to help her ace the test.

Sasasegawa Sasam and Rin continue to have battles, but that is pushed aside for as another one of her cats have brought her a mysterious message to help another student.

Kud shares an ancient island custom with Riki as she remembers the time she spent with her mother.

The Little Busters are there to help, but sometimes they are powerless to do anything.

Tebwa rebel forces are angry at the government and are looking for anyone connected with the space program to blame…

Rin next challenge has been delivered and Riki has grown more suspicious of the timing of the notes.

Kyousuke predictions of the final Little Buster member shocks Riki, but that is not the bombshell that will be presented to Riki.

Thrust into the role of leader of the Little Busters, Riki is finding it hard to fill Kyousuke shoes.

Kyousuke impliments a Battle Ranking system, with Riki slowly moving up the ranks, whilst Yuiko has fun teasing the other girls by giving them dubious advice. Meanwhile, a mysterious fighter known as Mask the Saito appears and starts defeating other members of the Little Busters and moving to the top of the rankings. Mask the Saito then confronts Riki in a battle, but he is stopped by a moving story by Komari and admits defeat, revealing himself to be Kyousuke, who passes the mask onto Riki.

While Riki Naoe goes to the classroom to pick up a Japanese lit notebook at nighttime, he is approached by Saya Tokido, who urges him to flee. After he hears a distant gunshot, he finds her abandoned student handbook left in the classroom.

This anime adapts Key's visual novel Kud Wafter, which follows the romantic relationship between Riki Naoe and Kudryavka Noumi from the game Little Busters!