After the Little Busters lose their first baseball game, the team decides to hold a pancake party. It has been nearly a semester since Kyousuke Natsume returned. As is customary, Riki Naoe continues to assist the Little Busters' members—both old and new—in facing their inner struggles. However, strange occurrences begin to take place, drawing Rin Natsume and Riki closer to uncovering the truth behind the "secret of this world." Rin and Riki are unaware that their discovery will ultimately alter the peaceful daily lives established by the Little Busters forever. Little Busters!: Refrain provides a conclusion to the colorful stories of its ensemble cast—shaped by the weight of emotions and reinforced by the bond of friendship—as they come to terms with their regrets and weaknesses.