"Kure-nai" centers on Shinkurou Kurenai, a 16-year-old conflict negotiator who resolves disputes in Tokyo's underworld. His life takes a dramatic turn when he is tasked with protecting Murasaki Kuhouin, a seven-year-old girl from a powerful and wealthy family. Murasaki has been sheltered her entire life, and her sudden introduction to the outside world creates a stark contrast between her innocence and the harsh realities Shinkurou navigates daily. The series explores their evolving relationship as Shinkurou becomes both a protector and a mentor to Murasaki, helping her adapt to a life far removed from her privileged upbringing.

The narrative delves into the complexities of Shinkurou's profession, revealing his connections to the criminal underworld and the moral ambiguities he faces. Murasaki's presence challenges his worldview, as her naivety and curiosity often clash with his pragmatic and sometimes cynical outlook. The story also introduces supporting characters such as Benika Juuzawa, Shinkurou's mentor and a formidable figure in the conflict resolution business, and Tamaki Mutsu, a close friend who provides emotional support and insight into Shinkurou's struggles.

As the plot progresses, the series uncovers the reasons behind Murasaki's need for protection, tying her fate to the power struggles within the Kuhouin family. Themes of family, loyalty, and the clash between innocence and corruption are woven throughout the narrative. The dynamic between Shinkurou and Murasaki serves as the emotional core of the series, balancing moments of lighthearted humor with darker, more introspective elements. The story ultimately examines the impact of their bond on both characters, as they navigate a world filled with danger, intrigue, and moral complexity.