Riki was a child when his parents died, leaving him hopeless and depressed. What saved him was a group of four kids calling themselves the Little Busters. They took Riki out and played with him during his time of need. He really enjoyed being together with them, and his grief gradually faded away. Now in his second year of high school they still hang out, fight and live together, and enjoy their school life.
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.