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. Some time later, Riki and the others learn that someone had filled Kudryavka's bag with thumbtacks and destroyed Komari's notes. Suspicious of a girl who was overhearing them, Riki follows her and finds the same girls Yuiko had noticed the other day in a classroom, figuring that they are the culprits. Despite being confronted by Riki, the girls claim that there is nothing he can without any evidence of what they did, until Yuiko appears and plays a recorded conversation between them that proves their involvement. Despite that, the girls refuse to give up and claim that they will keep tormenting Yuiko's friends until Yuiko destroys the room's door with a single kick and threatens to do the same with their faces, forcing them to give up. When a teacher arrives and discovers the damage, Kyousuke and the other boys cover for Yuiko and Riki as they escape by themselves to the broadcast room. The room seems familiar to Riki despite never having been there before and with his memories confused, he suffers another attack of narcolepsy and collapses.

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. Believing that he has fallen in love with her, they decide to have him lure the girls to the school building as they prepare a fireworks show for them, with instructions to find a way to get alone with Yuiko to set up the mood for his "confession". Wondering if he is actually in love with someone, Riki does as they say, but ends up alone with Yuiko by accident when the fireworks begin. The following day, Riki realizes that the same events of the previous day are being repeated as the date is also the same, June 20.

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. However, Riki learns that Yuiko is the only other person who knows the truth and she claims that it all is her fault. Her wish for staying with the Little Busters forever had been granted in the form of a dream, and she tells Riki that she only knew what happiness was after meeting Riki and his friends. Yuiko tells him that things will return to normal when he wakes up from the dream, but Riki will forget everything that happened. Before bidding farewell, Yuiko warns Riki to take care of Rin, as the "fated day" is at hand.

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, and upon learning what happened, Kyousuke reveals that a third-year student had also confessed to Rin, but he helped her decline him. Later that day, Rin asks Riki to help her buy some cat food and on the way back, she suggests they start dating and Riki agrees after confirming that she likes him. Riki has trouble trying tell Kyouske about it the next day, but Kyousuke claims that he already knew about it. Riki and Rin later tell the rest of the Little Busters, who congratulate them, but Riki chases after Rin after she runs away embarrassed. The white cat Lennon brings them another mysterious letter telling them that they have one final task to do before "learning the truth of the world", which is to "volunteer themselves during homeroom".

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. Riki at first asks Rin to decline their invitation, but he later realizes that this could be an important experience for her to grow as a person. However, when Riki tries to encourage her to take part in the program, she gets angry at him and ultimately accepts the invitation. On the eve of Rin's departure, Riki realizes that all the tasks they received helped her to mature and improve her confidence. He concludes that it was all a part of Kyousuke's plans, including inviting Komari and the other girls to become part of their group. His suspicions are confirmed when Riki finds Lennon with Kyousuke and then he confronts him about the "truth of the world" he mentioned in his letters. However, before getting some answers, they are forced to run away after being caught outdoors during curfew and when Riki trips over, Kyousuke disappears in front of him.

After Riki and the others after 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". Concerned for Rin being isolated, Riki decides to go after her, but he is stopped by Kyousuke, who makes a deal that he will bring her back for weekends only.

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 no where to be found. The result of the fight leads to Kengo fracturing his right arm, putting him out of commission for kendo practice; Kengo asks Riki to think of something fun all of them could do together. Rin is now afraid of everyone but Riki, who routinely drops her off at a local elementary school during the day. Meanwhile, Kyousuke is depressed and stays cooped up in his room reading manga. Initially unsuccessful to find something Rin enjoys to do, he eventually discovers her affinity for playing catch. Riki tries to invite Kyousuke to join in, but he refuses. Riki also invites Masato and Kengo to play a baseball game, but Kengo angrily refuses to participate, and Masato leaves shortly thereafter. Knowing the others are hiding something from him and Rin, Riki resolves to become a leader like Kyousuke and reform the Little Busters.

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 classmates and comes with a trap to catch him. However, the trap fails to restrain him fully and he starts pursuing them, after setting another trap with Rin's help, Riki manages to wear down Masato to the point of being able to defeat him barehanded. The knocked down Masato then reminisces that before meeting Kyousuke, he used to be treated as a fool by his peers until he trained his body enough to beat down whoever insulted him, but became isolated because of it, until Kyousuke appears and defeats him also using traps, leading to them becoming friends. It is also revealed that the reason for his rampage at school was because he suddenly started seeing everyone else as himself and believed that he could only become his own person by becoming the strongest of them all. After renewing his friendhip with Masato, Riki realizes that he must eventually defeat Kyousuke as well for his and his friends' sake, while a serious Kengo watches over him from afar.

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. Rin learns from Masato that Kengo originally joined the Little Busters after Kyousuke defeated his father in a kendo match. This leads Riki to challenge Kengo to a baseball match instead, with the first one to strike a home run being the winner and Kengo rejoining the Little Busters should he lose. After several attempts, Riki manages to land a home run but is too exhausted to throw the ball, so Rin takes his place. Rin's throws are fast but with initially no control, and when she manages to throw the ball properly, she succeeds in having Kengo strikeout, winning the match. Kengo rejoins the Little Busters, determined to follow Riki as long as he can.

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 was created by his spirit with the purpose of preparing both Riki and Rin to live without him and the others, as all of them except the pair apparently perished during an accident. Since then Kyousuke created an alternate timeline that was always reset when Riki or Rin had fallen into despair. However, Kyousuke's power to maintain this realm is waning, leading to the strange events occurring in the previous loop, and the departure of the other girls. When Riki and Rin ran away after she broke down from being separated from the others, Kyousuke was losing his faith, until Riki managed to establish himself as the leader, and once reunited with his friends, Kyousuke claims that the time for him and the others to bid farewell to Riki and Rin is at hand.

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 that the world they are currently in was created by him and the others after a bus accident killed all students aboard except for Riki and Rin and to prepare them to move forward with their lives, they put the duo on a series of trials to have them mature and become stronger. After Masato and Kengo bid their farewells, Kyousuke instructs Riki to take Rin past the school gates back to the real world, as the time for them to part has come. As Riki and Rin get past the gates, Kyousuke has one last tour arround the school before sitting on his desk and disappearing along the world he created.

Riki and Rin awaken in the real world and reminisce that during their field trip, their bus got into an accident and Masato and Kengo used their own bodies to protect them. Despite 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. Meanwhile, Rin has a meeting with Komari and the other girls in spirit and wishing to not part ways with them, she decides to look for a way to save them as well.

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, leaving the duo no other option but to pick him up after carrying all the others to safety. The bus explodes just after Riki and Rin return to rescue Kyousuke, but the incident ends with no deaths. Three months later, all of the students have returned from the hospital except Kyousuke, who is still in a coma, and the other Little Busters spend their days together, waiting for him to return. Once Kyousuke finally returns, the Little Busters have their own, private field trip to the beach together.