In a future where humans coexist with advanced robots known as gynoids, the story follows Batou, a cybernetically enhanced detective of the elite Section 9 security force. After a series of gynoid malfunctions that lead them to murder their owners, Batou and his partner, Togusa, are tasked with unraveling the mystery behind these violent incidents. Struggling with his own artificial existence, Batou delves into the seedy underbelly of the technologically-saturated world, trying to find the reason for the malfunction of the robots, which were designed to serve humans. The investigation takes on a personal turn as he encounters echoes of his past and glimpses of a spiritual world that challenges his beliefs about life and artificiality.

As their investigation deepens, Batou and Togusa discover a connection to Locus Solus, a powerful corporation involved in the manufacturing of the gynoids. The trail leads them through philosophical debates and encounters with enigmatic characters who force them to question the nature of consciousness and the soul. The crux of their search unveils a disturbing form of cybernetic crime tied to the essence of what it means to be human. The evolving mystery presents a complex web of corruption, ethics, and existential reflection on the fusion of human and machine. Batou's struggle with his own synthetic identity and humanity forms a significant thread that weaves through the overarching narrative of technological evolution gone astray.