Riki Naoe lost both his parents when he was a child, leaving him isolated and despairing. What pulled him from that darkness was a group of four children who called themselves the Little Busters: the charismatic and scheming Kyousuke Natsume, his quiet and antisocial younger sister Rin, the loud and muscle-headed Masato Inohara, and the stoic but reliable Kengo Miyazawa. They brought Riki into their games and adventures, and his grief gradually faded. Now they are all students at the same high school—Riki, Masato, Kengo, and Rin in their second year, Kyousuke in his third—and they still spend their days together, laughing and causing harmless chaos.

As their carefree school days begin to feel finite, the group decides to recapture their childhood spirit by forming a baseball team, also named the Little Busters. They start recruiting new members, including the cheerful but clumsy Komari Kamikita, the Russian exchange student Kudryavka Noumi, the cool and teasing Yuiko Kurugaya, the energetic Haruka Saigusa, and the quiet bookworm Mio Nishizono. Each new recruit carries her own personal struggles, and Riki, who suffers from narcolepsy, finds himself drawn into helping them resolve their inner conflicts.

Beneath the surface of friendly baseball practice and school life, strange events begin to occur. Rin receives mysterious letters from her cat, Lennon, instructing her to complete various tasks in order to uncover the secret of their world. These tasks lead the group into surreal and sometimes dangerous situations, hinting at a hidden truth behind their seemingly ordinary existence. The manga adapts the central storyline from the original visual novel, blending comedy, heartfelt drama, and a growing sense of mystery as the bonds between the characters are tested and deepened.