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 returning to pick up a notebook at his classroom during nightime, Riki is approached by a girl who urges him to flee. He does as she asks, but after hearing a gunshot, he turns back and finds an abandoned student ID. In the next day, Riki returns the ID to Saya Tokido, a student from the same year as him, and later is invited by her to meet him at the rooftop. When Saya meets Riki, she declares that she must dispose of him, or the "Darkness Executives" may discover her identity. Saya then attempts to have Riki fall from the roof, but when Masato appears, Riki manages to escape by having his friend catch him. Believing it must be another of Kyousuke's pranks, Riki inquires him about the Darkness Executives, and his friend asks him to not involve himself with them, as not even Kyousuke can oppose them for the sake of Rin's safety. After Saya fails to kill him in two other occasions, Riki being saved in the nick of time by Kengo in one of them, she decides to ask for his help instead, revealing that her mission is to locate a "secret treasure" inside the school. The duo then look for clues together when they spot a mysterious contraption inside a classroom, and after Riki figures out how to activate it, a secret entrance is revealed. Riki and Saya then pass through the entrance, fleeing from the Darkness Executives who appear to attack them.
Saya and Riki decide that before they venture any further to finding the 'treasure', they must first top up with supplies of food and drink, as they do not know what is ahead of them. They do some shopping and looking around town, which excites Saya, much to Riki's interest. Eventually they return to Saya's treasure hunt mission. After running into a some trouble with the Executives of Darkness, they find a bath, which Saya awkwardly undresses and gets into. They then have a picnic, when a sudden realisation hits Riki that they had met before in the past, and had been in love.
While Riki and Saya are walking through the dungeon, Riki is reminded of the fact that he was in love with Saya. However, Saya interrupts his thoughts, saying that he distracts him. At that moment, she trips and falls down. Saya tells they need to pull a rope to advance to the next level; however the rope is located to high to reach. So Saya needs to stand on Riki and jump in order to pull the rope. However they also need to defeat a gigantic golem in order to advance to the next level. While Saya is distracting the golem; Riki is trying to find a way to defeat it. Riki finds a sword, and taunts the golem to attack him. Saya climbs on the golem's head; and finds a key-hole on top of its head. Riki throws the sword to Saya, who inserts it into the keyhole, which destroys the golem. However, Saya falls down and hurts her leg. Riki carries her to the next floor. Saya confesses to Riki and tries to kiss him. Surprised, Riki does not accept the kiss. Saya says she will either kill him or kill herself because he rejectd her. But Riki says he also loves her and kisses her. Next level of the dungeon; Riki and Saya have to descent a slope using ropes. Saya almost falls because of her leg, but Riki saves her. They start talking about love; which embarrasses Saya and distracts her, which makes her fall down. However Saya seems unharmed, so they continue. Since now they are close to treasure; Saya starts talking about the treasure and says it's not an ordinary treasure like money or gold. Riki guesses the treasure is a part of an UFO; but Saya thinks it's a time machine. They only have to defeat the leader of the Darkness Executives, Shun Tokikaze to reach the treasure; who arrives at that moment. Riki readies his gun, but Saya stops him; telling him that she needs to defeat him alone. Shun Tokikaze leaves, and Saya follows him. Riki tries to follow them but is blocked by bars. Saya promises that they will go on a date, and leaves. Saya fights with Shun, but is killed. A game over screen is shown; and Saya says she already died 99 times. Saya chooses to "replay"; and everything starts over again with Riki and Saya meeting again in the hallway.
It is revealed that Saya's father works as a doctor and while at work overseas, she was taken with him and she was given a manga which she treasured dearly. When she returned to her hometown, she meets Riki and they play ball together until it starts to rain. On the way home, a mudslide seemingly kills Saya, but not before she enters the artificial world Kyousuke created. She is repeating the same scenario, and dies every time, thus making Kyousuke rewind time. In one of the replays, Saya and Riki face Tokikaze Shun, the antagonist of the manga Saya loved so much, which, coincidentally, Saya is the protagonist of the same manga. Using Riki as a decoy, she defeats Shun and goes to the 60th floor of the basement to receive the treasure. In a flashback, Saya reasons with Shun to let her replay her scenario one last time, and, because in the manga, the treasure wasn't revealed yet, requests Shun to make the treasure a biological weapon. Arriving at the 60th floor, Saya locks herself in a room and Riki witnesses Saya shoot herself in the head. Riki then wakes up, and Kyousuke tells him that the Executives of Darkness "jumped the gun" and that the treasure was a time machine. In the epilogue, it is revealed that Saya, back to when she was a little girl, did not die in the mudslide. She tells her dad of a dream that she had, and, when she later recovers, she goes outside to play with Riki.
In order to aid in the development of the Little Buster's Baseball Club, Kyousuke requests that Riki assist the dorm head with some paperwork. After arriving, Riki is surprised to find Kanata, and soon after the dorm manager sets off on an errand leaving the two alone. After completing their work, Riki and Kanata discuss the necessity to protect those they care about. The next day, Riki continues to aid dorm head. Yada Yada, Kanata meeting in secret with spy from Saigusa family. Kanata runs into home economics classroom to extinguish fire, where her clothing is drenched in water from sprinkler system revealing scars from beatings on her arms. She runs off into the yard trailed by Riki and Haruka.
Awakened early in the morning by someone announcing the return of Kyousuke Natsume, Riki Naoe goes to stop his roommate Masato Inohara from fighting their friend and Masato's rival Kengo Miyazawa. Riki asks Kyousuke to intercede, who tells them to fight only with objects thrown from the crowd of onlookers. Kyousuke's younger sister Rin objects when Masato tries to use a white cat as his weapon, causing Kengo to lose interest. Riki reminisces how he has been friends with Kyousuke, Masato, Kengo and Rin since childhood when they brought him into their group called the Little Busters. Riki later suggests that the five of them do something together like they used to, and Kyousuke proposes that they play baseball under the team name Little Busters. Kengo immediately excuses himself from this, as he has to prepare for a kendo tournament. Later that night, Kyousuke gets Rin to go to the girl's dormitory to try to recruit team members. After a couple of failed attempts, Rin is confronted by Sasami Sasasegawa and three other members of the softball team; Rin ends up losing the fight. The next day, Riki goes looking for new Little Busters members, which leads him to follow a girl up to the school's roof.
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.
The members of the Little Busters baseball team have morning practice, though Rin is less than enthusiastic. Masato gives Riki back his idiom dictionary, albeit damaged and smelly, in a plastic bag. Haruka Saigusa, a girl from a different class, wantonly borrows the dictionary before Riki can stop her, and upon chasing after her accidentally runs into the desk of Yuiko Kurugaya, a genius girl who is often absent from class. While during a class break when Riki is trying to buy a drink from a vending machine, Yuiko drags him away to a spot with a few chairs and a wooden box she set up among some hedges. They spend time talking, and ultimately Riki loses track of time, later dashing back to class when he hears the bell. Haruka gives Riki back the dictionary and berates him over its disgusting state under the cover. When Masato and Kengo are about to have another fight, Yuiko intervenes, causing Kengo to lose interest. Yuiko and Masato initially fight with the rules Kyousuke previously set up, but Yuiko loses after she severely kicks Masato several times. Later, Yuiko catches the Little Busters during practice and joins the team, proving to be a powerful asset.
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.
Riki sees the girl who looks like Mio in the courtyard, but she disappears soon after. Mio remains absent from school for several days, and people around Riki start slowing forgetting about her. The next day, Riki finds Mio in the courtyard, who gives him her treasured book of poems and invites him to go with her to the beach. Midori, the girl who looks like Mio, shows up at the beach and reveals that the reason why Mio always carries a parasol is to hide the fact that she has no shadow. Upon learning this, Riki suffers an attack of narcolepsy, and when he wakes up, he is already back in his dorm room, but cannot remember what happened at the beach. Life returns to normal, until Riki rediscovers Mio's book of poems and goes to look for her in the classroom. However, Midori comes in and everyone except for Riki know her as Mio. While mulling over Mio's disappearance, Midori confronts Riki and wants him to call her Mio like everyone else, which Riki refuses. Midori points out that she also does not have a shadow, and Riki thinks that Midori may be Mio's shadow. Midori says that eventually, he too will forget about Mio.
Riki is resolute that he will not forget about Mio, but Midori plays around with his memories of her, leaving him unsure about how much of his memories of her are real. Riki seeks help from Kyousuke, but all he can offer is to tell Riki to not trust anyone but himself for the sake of Mio. Riki suddenly remembers Mio saying she was going to submit a tanka in the school's competition, and discovers that the poem is about the conversation they previously had about the paper airplane. After talking with Midori, Riki realizes Mio is at the beach, where the two reunite. Mio tells Riki how she first "met" Midori as a child, who is in fact an imaginary little sister she created. Mio's mother eventually gets her medical treatment until she finally forgets all about Midori. However, she remembered her after reading the tanka by Bokusui Wakayama about the bird and the ocean, which caused her to black out. After she came to, she realized her shadow was gone. Riki pleads with Mio to come back with him, but she refuses and turns into a bird, flying away. Riki begins to sob over losing her, but is reinvigorating after receiving a call from Midori. Riki goes into the ocean and locates her, where he once again pleads for her return and ultimately witnesses Mio and Midori becoming one person. Afterward, the two find themselves back on the beach, and Mio has her shadow back. They go back to school and rejoin the rest of the Little Busters.
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. After eating some pastries, the girls take turns bathing until Riki is last. However, he later finds his clothes have been replaced by a girl's uniform, which he reluctantly puts on. The resident assistant of the girl's dormitory drops by to tell them to keep the noise down if they do not want a visit from the disciplinary committee. Afterward, they rolls up some newspapers and start hitting each other, which ultimately causes Kanata and several other disciplinary committee members to warn them about being too loud. Luckily, Kanata does not recognize Riki while he is cross-dressing. The next morning, Riki leaves after thanking Yuiko for helping Rin socialize with the other girls. He runs into Kyousuke who had just won the right to go rescue him after playing games the whole night.
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.
Haruka tells her friends how she and Kanata were born from two separate fathers, one of whom, Shō Saigusa, was the one previously arrested. Due to this, the Futaki family took control of the Saigusa family, and Haruka and Kanata were compared from early on to decide which one of them would be the heir to the family. After Kanata was chosen to be the heir, Haruka was blamed and tormented by the family, so Haruka chose to make trouble for Kanata so that she would get scolded for not keeping her in line. Haruka initially believes her friends will abandon her after knowing the truth, but they resolutely reassure her that they would never abandon her. Later, the Little Busters play baseball until Haruka is able to smile again, though afterwards Kanata warns her not to drag her friends into any trouble. Another day, Haruka bakes chiffon cake, but it turns out dry. Haruka goes see Shō to find out if he is in fact her father, but he does not tell her. Later that night, Riki tells Kanata that he just wants to help Haruka like he was helped in the past, but he apologizes for his arrogance. The next day, Haruka shows Riki some chiffon cakes she baked, and he is surprised at how much better they taste this time. However, it turns out that this was merely Kanata disguised as Haruka, who suddenly shows up shocked.
As it begins to rain, Haruka confronts Kanata and discovers that Kanata had lied to her when they were younger about being allergic to eggs. After Kanata leaves, Kudryavka tells Riki that she is a nice person when inside their room, and merely pretends to usually be cold. Riki finds Kanata in a classroom and she tells him how she told Haruka she was allergic to eggs to protect her from getting beaten by their family, but Haruka finds it difficult not to shoulder all of her hate onto Kanata. Later, Riki convinces Haruka to go talk to Kanata, and she tells her she wants to know the truth about their family. Though initially reluctant, Kanata tells Haruka that their family was nice to her as long as she was better than her, and that the Futaki family often beat Kanata whenever she went easy on Haruka. Kanata had to secure the succession of the Saigusa family and be hard on Haruka, or else they would have killed Haruka. Haruka apologizes for thinking that she was the only one having a hard time, and she reconciles with her sister. Kanata decides to leave the family and the two go see Shō, who tells them their mother and their other father tried to leave the family with Haruka and Kanata, but the Saigusa family took the kids back, prompting Shō to intercede and ultimately go to jail as a result. Haruka tells him that she does not have to know who her real father is anymore, and later, Haruka and Kanata go see their mother and other father.
Kudryavka decides to take a national proficiency test in school, and the other Little Busters members help her study, especially in her weakest field English. Komari coaches Kudryavka in English, followed by Mio covering both math and physics. While Kudryavka is eating with Riki and Masato, some girls make fun of her, but are quickly scared away by Yuiko. Kudryavka continues to study in the library with Riki, Masato and Yuiko. Kudryavka tells them about her grandfather who raised her and how she used to travel around with him, including a small island nation called Tevua in Southeast Asia where she was born. Kanata comes by to give Kudryavka back her book on the many-worlds interpretation, one of many books she reads for international exams as a hobby. On the day of the test, Kudryavka accidentally fills in the wrong bubbles on her test, and has to take a remedial class as a result. Kudryavka feels bad about failing after her friends helped her study so much, but the others Little Busters show up in the remedial class to show her that she is not alone.
Another mysterious letter arrives for Rin and Riki, telling them to ease the lovesickness of a second-year boy named Aikawa who likes Sasami. They start by asking Sasami what her hobbies are and the type of guys she likes, only to find out that she likes Kengo, though he has no interest in her. Aikawa is shocked to hear Sasami likes Kengo, but Rin urges him to sing a hip-hop song to Sasami with some original lyrics to imply his love for her. Aikawa accidentally messes up the last line in the song, leading Rin to suggest a three-way attack on Kengo to get Sasami to fall for Aikawa. However, this backfires and Kengo ends up taking down Aikawa. Sasami arrives on the scene, impressed by Kengo's athleticism. Aikawa decides to give up, and Riki later realizes that they merely have to ease the pain of his unrequited love to fulfill the request. Rin goes to apologize to Sasami, who ultimately agrees to hand over her email address after sympathizing with what Aikawa is going through. Rin gives her email to Aikawa, who thanks her for it.
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.
Riki and Rin are by the side of the river when they receive another mysterious letter telling them to do a puppet show, and soon spy some kids having an argument. A girl was going to put on a puppet show for her friend, but the panda doll she was going to use got damaged. Wanting to clear the task, Rin tells the kids she will put on a puppet show the next day. Rin initially gets help from the rest of the Little Busters, but after Kanata calls curfew and sends them back to their rooms, Komari secretly comes over to Rin's room to finish the preparations until the following morning. Rin takes everything back to the spot by the river where she tells Riki that she should try hard to do the show by herself because Komari helped her so much. The five kids from the previous day show up and Rin puts on the show for them which they all enjoy. Rin goes to see Komari, but initially has trouble finding her until she finds her up on the school roof. Komari congratulates Rin for a job well done and tells her she was wishing on a star for success. Komari says the star-shaped hair ornament she wears is also a wishing star that may grant her wish, and when Rin points out that she has two, Komari says that the other star will be for granting Rin's wish.
Kyousuke tells the Little Busters that their first baseball game will be against a team composed of captains from other sports clubs. Most of the team is ultimately excited about the match, save for Riki and Rin. In addition, Masato points out that they still only have eight members, but Kyousuke reassures them that they will eventually have the final member. Later, Riki, Rin and Masato spot Kengo talking with Miyuki Koshiki, a former member of the archery club who was forced to quit after she lost an eye during an accident. Masato brings this up during lunch, brewing speculation from others about their relationship, but Miyuki points out that she was just asking him for advice. Later that day, Riki and the others learn Miyuki went up to the edge of the roof, prompting him, Rin and Masato to rush there against orders to stay inside the classroom. Three teachers try to dissuade her, but Miyuki slips and falls in the commotion, just to be rescued by Kengo in the nick of time, although he breaks his left arm and is suspended from the kendo club for a semester. Kengo decides to join the Little Busters, and after several tries, manages to hit a home run with one arm. With the Little Busters team complete, Naoe cannot shake the suspicion that Kyousuke was aware all this time that Kengo would eventually join them, as if he knew in advance what would happen.
After being left in charge of the Little Busters, Riki is struggling about what he should do since he no longer has Kyousuke to lead him, Kyousuke himself explains Riki he is now stronger than ever and all the things he's done, wether he realised it or not, proved that he was stronger than he believed he would be, Kyousuke leaves, telling Riki to become stronger. In the club room, still struggling, Riki gets encouragement words from Haruka and Mio who explain how Riki saved their lives. On the rooftop Kurugaya, Komari and Kudryavka also explain how Riki helped them overcome their problems and saved their lives. With all this in mind Riki comes up with a strategy to defeat the oponents' team. During the game the team is being watched by all their friends (even Sasami and her minions) and successfully defeats the other team, leaving them victorious as the Little Busters. After the credits some scenes are shown that are similar to the Little Busters visual novel's Refrain route after Kyousuke's plan went into action. They depict Rin leaving the school and Kyousuke and Kengo fighting in the rain after their baseball match. The episode ends with the title screen of "Little Busters Refrain" (the visual novel's final route) and Kyousuke's voice saying "The time that had stopped begins to move once more" implying there is still a secret to this world to be discovered and the story is not over yet.
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. When Rin come back the following weekend, she is depressed and stays in bed. Riki goes to Kengo for advice, who tells him he has to fight Kyousuke to keep Rin from going back to the school. Kyousuke agrees to settle it over a baseball game with Masato as his partner, but Riki and Kengo ultimately fail. Kengo claims that Kyousuke rigged the game and punches him before being restrained by Riki and Masato. The next morning, Riki tells Rin that they are running away together. They travel to a house in the country where they played as kids, but they are eventually discovered by the police who raid the house.
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.