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...

On the school's roof, Riki finds Komari Kamikita, a clumsy girl from his class who loves sweets. Riki tells her he wants to recruit her for the baseball team, but he soon realizes that she may not be well suited for baseball. Later, Riki goes to find Rin after she shirks her classroom duties to play with several cats. One of the cats has two notes tied to it, the first of which says that there is a secret to the world and if they want to find out what it is, they have to complete several tasks first. The second note lists their first task: Fix the sanitation problem in the boys' dorm storage shack. Riki doubts the sincerity of the notes, but Rin is excited to take on the first task. She later gathers up Kyousuke, Riki and Masato to go clean the storage shack. Komari finds them there and agrees to be join their baseball team, but first she and the others go to work cleaning up the shack. On the baseball field, Komari displays a complete lack of athletic ability, but Kyousuke still welcomes her onto the team after she replies to his question of what is necessary for baseball with the answer, "Guts, bravery and friendship." Soon after, Riki collapses from an attack of narcolepsy, which he has had since childhood.

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.

Riki helps his classmate Kudryavka Noumi move her boxes into her new dorm room one afternoon. The next day, Riki goes to the roof looking for Komari to thank her in place of Rin for taking care of one her cats that was injured. He finds her asleep and hears her sleep-talk about her brother, but when Riki asks Komari about him, she says she is an only child and that her brother only appears in her dreams to read her a picture book with eggs and chicks. The next day, Riki and Rin go to the roof and find Komari a little sad. She had found the picture book from her dreams with the name Takuya Kamikita on the back, but her mother will not tell her anything about having a brother, and Komari cannot remember anything about him. Komari asks Riki and Rin to accompany her to a retirement home, and the other members of the Little Busters decide to join in as well. They spend time with the retirees, talking with them and cleaning their rooms. Riki cleans the room of a cross old man named Kojirō who normally scares anyone away by yelling at them, but Riki stays and cleans his room regardless. After he scares away Komari, Kojirō reveals his full name to be Kojirō Kamikita and tells Riki to keep her away from him.

Komari continues to dream about her brother, and Riki goes to see Kojirō to learn more about Takuya. Kojirō merely tells him that he should not pry further into the matter if he cares about Komari. Unable to sleep, Riki goes out to buy a drink and encounters Komari at the school gate, who had gone out to buy snacks. She invites him up to the roof to watch a meteor shower, where the spend the rest of the night. Komari asks Riki to go on a date with her so she can search for her lost memories. They take a train to go to where Komari used to live and they end up taking a boat out on a lake. Riki suggests to her that she does not necessarily have to look for her brother, and Komari jokingly asks him if he will be her brother. It starts raining on their way back towards school, and while running to find shelter, Riki spots a dead kitten. Komari starts sobbing uncontrollably as she recalls memories of her brother.

Komari is in shock from remembering her dead brother Takuya, recalling the time they spent together in the hospital. In Komari's recollection, Takuya writes a picture book for her, and tells her that he might be gone when she wakes, but tells her not to be sad because it will all be a dream. When Komari awakens, her brother has died, but she remembers what he said, and does not despair. As a defense mechanism, Komari begins to believe that Riki is her brother. Kyousuke tells Riki that if anybody can save Komari, Riki can. Riki speaks with Kojirō, who tells him that this happens every time Komari witnesses death, and that she will return to normal in a few weeks. However, Riki is determined to save Komari, and adds to Takuya's story book. Riki forces Komari to accept her brother's death, but through his extension of Takuya's book, shows Komari that she has friends to support her.

Riki sets out to find more members for the team.

Riki, Rin, and Masato go to great lengths to make sure their newest team member gets what she wants: a roommate.

Rin finds another message on Lennon. This time, the mission is to save the cafeteria. Later, Riki wonders how the message's author knew there would be a crisis in the cafeteria, just before he is hit by another narcolepsy attack...

Riki is tasked with finding the last member of the Little Busters to have a full baseball team of nine. Riki hits a foul ball that hits Mio and he brings her a compress the next day. He notices that Mio always has a parasol and that he always sees her reading under the same tree in the courtyard. Their other classmates call Mio "shadowless" because of the parasol and the fact that she does not have much presence. Riki wants to help her like Kyousuke and the others helped him, so he asks Mio if she would like to join the Little Busters, but she declines. Later, Yuiko enlists the help of Riki to help find Mio's book. They go back to the classroom, but are unable to find it, thinking that someone may have hidden it as a joke. However, Yuiko arrives to explain that there was no wrongdoing, and the girl who had picked up the book before gives it back to Mio. Some of the Little Busters members come to get Riki for practice and Mio goes to watch them play.

To test the team's courage, Kyousuke sets up various traps within the school.

Riki wants Mio to be included among his friends, so he asks her to be the team's manager, which she ultimately accepts after initially thinking they were starting an all-male idol group. After practice, Mio brings everyone hot drinks and they exchanges phone numbers with her. The next day, the Little Busters get together to write tanka poems, but Mio leaves part of the way through. Riki finds her sitting under her usual tree, and after talking for a bit, Riki feels as if Mio wants to disappear. Riki tells Mio that he saw someone who looked like her in town, but she was no carrying he usual parasol. Before leaving, Mio tells him that she plans on submitting a tanka in a competition held at school. The next day, Mio does not show up at school, and Riki overhears his classmates saying they also saw a girl in town who looked similar to Mio. After school, Riki sees the girl standing below in the courtyard.

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?

After an initial failed attempt by Komari and Kudryavka to get Riki to follow them because of something 'serious', Rin texts Riki to come to her room in the girl's dorm. Narrowly escaping detection by Kanata and the other disciplinary committee members, Riki makes it to her room to find the rest of the female Little Busters members together for a sleepover. Kyousuke calls Riki and surmises that he has been kidnapped by the girls, so he, Masato and Kengo play games to figure out which one of them will go to rescue Riki.

Masato battles Haruka after she eats some of his katsudon, but he loses quickly. Later, Riki, Rin and Komari watch as Haruka starts to repair a bench which she has fond memories of, but Kanata arrives and points out that the bench was already going to be destroyed so there was no point in trying to repair it. Haruka and the others watch as two other disciplinary committee members destroy the bench and take away the remains to be incinerated. Haruka is taken away to the disciplinary committee to answer for her numerous infractions, but she loses her composure from the committee members laying countless blame on her, including accusing her of wrongdoing she did not commit. Before she can make things worse for herself, Yuiko intervenes and calms the situation, though Haruka is still ultimately punished. Another day, the whole school is in an uproar after flyers are posted all around school saying that Haruka's father is a criminal. The members of the Little Busters go around school collecting and taking down the flyers until they finally find Haruka, who had been crying alone in the baseball clubhouse. She explains that in her family, each woman takes two husbands, and one of her mother's husbands was later arrested for murder and attempted arson. Finally, Haruka reveals that she and Kanata are in fact twins.

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.

After another training session, the Little Busters join up to clean their clubroom. Later in the night, Riki comes across Kudryavka and assists her with a traditional ritual of her country, Tevua, which was once part of the Soviet Union. During the ritual, Kudryavka tells Riki about her mother and how she spent little time with her as she was preparing herself to become an astronaut. Kudryavka also tells him that her name comes Laika, a Soviet space dog who became the first animal to orbit the Earth. When the day finally comes for her mother to launch into space, Riki goes to look for Kudryavka to watch it on TV with her. When he finds her outside, she feels that it is better not to watch it as her own manner of wishing good luck. However, Riki and Kudryavka later learn that the rocket exploded on launch, and that mission control has lost contact with Kudryavka's mother.

No news comes whether Kudryavka's mother is still alive, and travel is restricted to and from Tebwa to reduce risk of contamination from the exploded rocket engine. However, the Tebwan embassy sends Kudryavka a plane ticket so she can go to see if her mother is safe. Kudryavka is conflicted about going back to Tebwa because she had come to Japan to escape having dropped out of Tebwa's aviation school after half a year. Initially, Kudryavka decides to stay and throws away everything she had related to space, but Riki recovers the items and brings them back to her. Riki tells her that she can just be herself in chasing her dream of space, even if she cannot become an astronaut. Kudryavka admits that she wanted to see her mother and decides to go back to Tebwa. Before leaving, Kudryavka says goodbye to her friends.

As her friends in Japan learn that an uprising started in Tebwa following the failed rocket launch, Kudryavka meets her grandfather where he is in hiding and learns that her mother survived the explosion. As her grandfather leaves to pick up her mother, Kudryavka is captured by the rebels and imprisoned in a cave. As her friends keep wishing for her safe return, Riki holds on to the gear she left behind, a memento of her mother's, and it mysteriously appears in Kudryavka's hands, which she uses to break free. Some time later, the uprising is quelled and Kudryavka reunites with her mother for a while before she returns to Japan and rejoins her friends.

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.