Riki Naoe is troubled by the knowledge that his childhood friends will eventually go their separate ways as their leader, Kyousuke Natsume, begins job hunting. Sensing Riki’s unease, Kyousuke declares his intention to form a baseball team and names it the Little Busters. The core group, including the timid Rin Natsume, energetic Masato Inohara, and stalwart Kengo Miyazawa, sets out to recruit new members. As Riki works to gather teammates such as the cheerful Komari Kamikita and the composed Yuiko Kurugaya, strange envelopes containing "missions" or "tasks" begin arriving for Riki and Rin, sent by an anonymous sender. These tasks guide the group toward uncovering a hidden secret said to lie at the heart of the world they inhabit. The characters navigate both their daily school life with comedic and heartfelt moments and deeper personal conflicts among the new members, all while the mystery of the endless refrain and the true nature of their reality slowly comes into focus. The story builds toward the revelation that this world is not as logical or permanent as it seems, and the bonds of the Little Busters are tested as the truth approaches.