Following the Little Busters after they lost their first baseball game, the team decides to have a pancake party. It has been almost one semester since the return of Kyousuke Natsume. As usual, Riki Naoe continues to help the Little Busters' members—both old and new—with confronting their inner struggles. However, strange happenings begin to occur, leading Rin Natsume and Riki closer to unraveling the truth behind the secret of this world. Little do Rin and Rikki know, their discovery will end up changing the peaceful everyday lives created by the Little Busters once and for all. Little Busters!: Refrain brings a conclusion to the colorful stories of its ensemble cast—forged with the weight of emotions and strengthened with the bond of friendship—as they come to terms with their regrets and weaknesses.

After the National Tournament, the Seidou High baseball team moves forward with uncertainty as the Fall season quickly approaches. In an attempt to build a stronger team centered around their new captain, fresh faces join the starting roster for the very first time. Previous losses weigh heavily on the minds of the veteran players as they continue their rigorous training, preparing for what will inevitably be their toughest season yet. Rivals both new and old stand in their path as Seidou once again climbs their way toward the top, one game at a time. Needed now more than ever before, Furuya and Eijun must be determined to pitch with all their skill and strength in order to lead their team to victory. And this time, one of these young pitchers may finally claim that coveted title: The Ace of Seidou.

Shinobu Oomiya once left Japan to participate in a homestay in England. During her time there, she became close friends with Alice Cartelet, the daughter of the family she was living with. However, when it was time for Shinobu to return to Japan, the two were able to express their sorrow despite the language barrier between them. Five years later, now a first year student in high school, Shinobu receives a letter by air mail in a language she does not understand. This letter is penned by none other than Alice, detailing her own homestay in Japan. In fact, Alice will be attending Shinobu's high school and living with her! Alongside their friends Youko Inokuma, Aya Komichi, and Karen Kujou, the five girls attend school together and learn about what their different cultures have to offer, day after day.

The innocent Nagomi Wahira has always admired the cute girls serving at maid cafes. Hoping to fulfill her dream of becoming one, she moves to Akihabara to work at the maid cafe Ton Tokoton. Nagomi's first day seems completely normal—until she has to run an errand at a rival maid cafe along with her fellow recruit, the mature Ranko Mannen. There, things quickly go south, and Nagomi soon gets her first taste of Akihabara's violent maid wars. As she watches Ranko calmly battle her way through a horde of gun- and knife-wielding maids, Nagomi realizes that maid cafes are drastically unlike what she had envisioned. While struggling to reconcile her expectations with the harsh reality she finds herself in, Nagomi searches for the enjoyment she once saw in the lives of maids.