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One night, as meteors streak across the star-studded sky, Shion Pavlichenko becomes a Contractor. Despite her brother's transformation, Shion's twin sister Suou continues to live a fairly ordinary life, attending middle school with her friends and getting caught up in the awkwardness of growing up. However, everything changes when her home is invaded by a masked man cloaked in black, destroying any sense of normality she once had. Revealed to possess latent Contractor abilities of her own, Suou is caught between family, friends, and her own sense of purpose as she ventures into the ruthless world of cutthroats and espionage that Contractors call home. Meanwhile in Tokyo, investigation surrounding Hell's Gate's sudden collapse is underway, and prophetic signs of doom point in the direction of a silver-haired doll. [Written by MAL Rewrite]

Fleeing from the consequences of his decision at the Hell's Gate, superpowered Contractor Hei and his companion Yin take refuge in a quiet inn, adopting the guise of a married couple in order to not draw suspicion. In an attempt to recover from recent events, Hei befriends the inn's other guests. He discovers that one of them is a fellow Contractor tasked with killing him. Their resulting encounter spells disaster for both Hei and Yin, who are forced to fight for their lives and grapple with the emotional wounds sustained in their previous life together. [Written by MAL Rewrite]

A side-story of Darker than Black, also called Episode 26, that takes place during the events of Kuro no Keiyakusha. The Syndicate has another job for Hei and his team. This assignment involves the sought after possessions of a dead contractor, which are believed to have been buried beneath a cherry tree. Meanwhile, Misaki Kirihara and her team plan a trip to the Cherry Blossom festival. [Written by MAL Rewrite]

It has been 10 years since Heaven's Gate appeared in South America and Hell's Gate appeared in Japan, veiling the once familiar night sky with an oppressive skyscape. Their purposes unknown, these Gates are spaces in which the very laws of physics are ignored. With the appearance of the Gates emerged Contractors, who, in exchange for their humanity, are granted supernatural abilities. In the Japanese city surrounding Hell’s Gate, Section 4 Chief Misaki Kirihara finds herself at odds with an infamous Contractor codenamed Hei. Called "Black Reaper" in the underground world, Hei, like his associates, undertakes missions for the mysterious and ruthless Syndicate while slowly peeling back the dark layers covering a nefarious plot that threatens the very existence of Contractors. From the mind of Tensai Okamura comes a sci-fi thriller taking the form of a subtle exposé on a war in which political positions and justice have no sway—a war waged exclusively in the shadows. [Written by MAL Rewrite]