"The Sky Crawlers" is set in an alternate reality where perpetual war is waged by corporations using young pilots known as Kildren, who are genetically engineered to never age beyond adolescence. These pilots engage in aerial dogfights as part of a commercialized conflict, providing entertainment and distraction for the public. The story centers on Yuichi Kannami, a new pilot assigned to the Rostock Corporation's base, where he joins a squadron of Kildren led by the enigmatic ace pilot Suito Kusanagi.

Yuichi quickly adapts to the routine of combat missions, but his curiosity is piqued by the mysterious circumstances surrounding Suito and her predecessor, a legendary pilot named "The Teacher," who disappeared under unclear circumstances. As Yuichi delves deeper, he uncovers unsettling truths about the Kildren's existence, their purpose, and the cyclical nature of their lives. The narrative explores themes of identity, mortality, and the ethical implications of creating beings destined for endless conflict.

The relationship between Yuichi and Suito becomes a focal point, as their interactions reveal layers of emotional complexity and shared history. Suito's stoic demeanor and Yuichi's persistent questioning gradually unravel the psychological toll of their existence. The story also examines the broader societal context, where war is commodified, and the Kildren are both celebrated and dehumanized.

Aerial combat sequences are a prominent feature, showcasing the technical prowess and strategic depth of the pilots. The battles are not merely action set pieces but serve to highlight the tension between the Kildren's youthful appearance and their grim reality. The series maintains a somber tone, emphasizing the futility and repetition of their lives, as well as the moral ambiguity of their creators and the society that exploits them.

The narrative builds toward a climactic confrontation that forces Yuichi and Suito to confront their roles in the system and the possibility of breaking free from its constraints. The ending leaves room for interpretation, reflecting the series' overarching themes of cyclical existence and the search for meaning in a world defined by perpetual conflict.