"Libra of Nil Admirari" is set in a fictional version of Taisho-era Japan, where cursed books known as "Tome of the Harbinger" cause emotional and psychological turmoil, often leading to death or destruction. These books, imbued with the intense emotions of their authors, are capable of influencing readers in dangerous ways. The story centers on Tsugumi Kuze, a young woman from a noble family who becomes involved with the Imperial Library Intelligence Asset Management Bureau, also known as "Libra," after her brother falls victim to a cursed tome. Tsugumi possesses the rare ability to see the "aura" of these books, a skill that makes her invaluable to Libra's mission to locate and neutralize them.

The narrative explores Tsugumi's journey as she joins Libra, working alongside its members to investigate and destroy the cursed tomes. The team includes Akira Matoi, the bureau's leader; Shouko Tatsuki, a skilled swordswoman; Shun Kagura, a former military officer; and Hajime Arisugawa, a mysterious and aloof figure with a personal connection to the tomes. Each member of Libra has their own motivations and backstories, which are gradually revealed as the series progresses. The group faces various challenges, including uncovering the origins of the cursed books, confronting individuals driven to madness by their influence, and dealing with the moral complexities of their mission.

As Tsugumi delves deeper into the world of Libra, she uncovers secrets about her own family and the true nature of the cursed tomes. The series balances episodic investigations with an overarching plot, revealing the broader implications of the tomes' existence and their connection to societal issues of the time. Themes of loss, grief, and the power of human emotions are central to the narrative, as the characters grapple with the consequences of their actions and the emotional weight of their mission. The story culminates in a confrontation with the mastermind behind the proliferation of the cursed books, forcing Tsugumi and her allies to confront their own vulnerabilities and the darker aspects of human nature.