Riki Naoe, a high school student, is the protagonist of "Little Busters!" After losing his parents at a young age, Riki finds solace in a close-knit group of friends who call themselves the "Little Busters." The group, formed during their childhood, includes Kyousuke Natsume, the charismatic leader; his younger sister Rin Natsume, a quiet and reserved girl; Masato Inohara, a strong and loyal friend; Kengo Miyazawa, a stoic and disciplined individual; and Komari Kamikita, a cheerful but somewhat naive girl. Together, they spent their childhood playing games and creating lasting memories.

As the story progresses, the group decides to form a baseball team to relive the camaraderie of their youth. However, their plans are complicated by the arrival of new members, including Haruka Saigusa, a mischievous and energetic girl; Kudryavka "Kud" Noumi, a half-Russian transfer student with a kind heart; Yuiko Kurugaya, an enigmatic and mature upperclassman; and Sasami Sasasegawa, a skilled archer with a mysterious past. Each character brings their own unique personality and backstory, which gradually unfolds as the series progresses.

The narrative delves into the personal struggles and emotional challenges faced by the characters. Riki, who suffers from narcolepsy, often finds himself in situations where he must support his friends through their difficulties. Rin, in particular, becomes a central figure as her relationship with Riki deepens, and her own insecurities and fears come to light. The series explores themes of friendship, loss, and the passage of time, as the characters confront their pasts and strive to overcome their personal demons.

As the story unfolds, a mysterious element is introduced through a series of cryptic messages and events that suggest a deeper, more surreal layer to the narrative. The characters are drawn into a series of challenges and games orchestrated by an unseen force, which tests their bonds and forces them to confront their fears. This leads to a gradual unraveling of the true nature of their reality, culminating in a revelation that ties together the various threads of the story.

The series balances moments of lighthearted humor and heartfelt emotion, creating a narrative that is both engaging and thought-provoking. The interactions between the characters are central to the story, as their relationships evolve and deepen over the course of the series. Through their shared experiences, the Little Busters learn the value of friendship and the importance of supporting one another through life's challenges.