"Darker than BLACK" is set in a world where a mysterious anomaly known as the Heaven's Gate appears in Tokyo, altering the sky and giving rise to individuals with supernatural abilities called Contractors. These Contractors possess unique powers but must pay a price, known as a Remuneration, each time they use their abilities. The story primarily revolves around Hei, a Contractor working for the Syndicate, a shadowy organization that employs Contractors for covert operations. Hei, also known as the "Black Reaper," is a skilled operative who maintains a calm and detached demeanor, often masking his true intentions.

The narrative unfolds across two main arcs. In the first arc, Hei is tasked with various missions that often involve espionage, assassination, and retrieval of sensitive information. Alongside his team, which includes Yin, a Doll with the ability to track individuals through electronic signals, and Mao, a Contractor trapped in the body of a cat, Hei navigates a morally ambiguous world where the lines between right and wrong are blurred. The missions gradually reveal deeper layers of intrigue, including the true nature of Contractors, the Syndicate's motives, and the origins of the Heaven's Gate.

The second arc shifts focus to a new protagonist, Suou Pavlichenko, a young girl who becomes entangled in the world of Contractors after her father, a scientist researching the Heaven's Gate, is killed. Suou discovers she has latent Contractor abilities and is pursued by various factions seeking to exploit her powers. Hei re-emerges as a key figure in this arc, now operating independently and driven by his own mysterious agenda. The story explores themes of identity, loss, and the consequences of wielding power, as Suou grapples with her newfound abilities and the moral dilemmas they entail.

Throughout the series, the narrative delves into the lives of various Contractors and their struggles with the dehumanizing effects of their powers. The Remunerations, often bizarre and personal, serve as a constant reminder of the cost of their abilities, highlighting the emotional and psychological toll on these individuals. The series also examines the broader implications of the Heaven's Gate and the global power struggles it has ignited, with governments and organizations vying for control over the Contractors and the secrets they hold.

"Darker than BLACK" combines elements of science fiction, noir, and action, presenting a complex and layered story that keeps viewers engaged with its intricate plot and morally ambiguous characters. The series is notable for its exploration of the human condition through the lens of its supernatural premise, offering a thought-provoking and immersive experience.