"Darker Than Black" is set in a world where an anomalous region known as the Hell's Gate appears in Tokyo, altering the sky and giving rise to individuals with supernatural abilities called Contractors. These Contractors gain extraordinary powers but lose their emotions and must pay a price, known as a "remuneration," each time they use their abilities. The story primarily revolves around Hei, a highly skilled Contractor who works as an assassin and spy for the Syndicate, a shadowy organization. Hei operates under the alias "BK-201" and is often accompanied by his partner, Yin, a Doll—a humanoid being capable of remote viewing but devoid of free will.

The narrative unfolds through episodic missions intertwined with a larger, overarching plot. Hei is tasked with various assignments by the Syndicate, often involving espionage, sabotage, or assassination. As the story progresses, it becomes clear that Hei is not a typical Contractor; he retains some semblance of emotion and humanity, setting him apart from others of his kind. His motivations and past remain shrouded in mystery, gradually revealed through flashbacks and interactions with other characters.

Key figures in the series include Misaki Kirihara, a determined police investigator who becomes entangled in Hei's missions, and Huang, a Syndicate operative who serves as Hei's handler. The series also explores the lives of other Contractors and Dolls, delving into their struggles with identity, morality, and the consequences of their powers. The plot thickens as Hei uncovers secrets about the Syndicate, the true nature of Contractors, and the origins of Hell's Gate.

Themes of loyalty, betrayal, and the cost of power are central to the narrative. The series balances action-packed sequences with moments of introspection, examining the blurred lines between humanity and inhumanity. As Hei navigates a world of shifting alliances and hidden agendas, his journey becomes one of self-discovery and redemption, culminating in a climactic confrontation that challenges the very foundations of the world he inhabits.