Little Busters! story revolves around the main protagonist Riki Naoe, a young male high school student.

When Riki was a child, his parents died, leaving him hopeless and depressed. What saved him was a group of three young boys and one girl his age who referred to themselves as the Little Busters—a group dedicated to fighting evil and preserving justice. The leader of the Little Busters was Kyousuke Natsume who had a younger sister named Rin. The other two members of the Little Busters were Masato Inohara and Kengo Miyazawa, who are rivals despite being friends. They took Riki out and played together with him during his time of need, effectively making him the fifth member of the Little Busters. In time, Riki really enjoyed playing with them, and his grief over his parents gradually faded away. When the story begins, Riki and his friends are seemingly in their second year of the high school they attend, except for Kyousuke who is in his third year. They still hang out together, and enjoy their school life.