On a sunny afternoon in her Paris apartment, assassin-for-hire Mireille Bouquet receives a strange email from Kirika Yuumura, a young student from Japan, inviting her to "make a pilgrimage to the past" together. Initially thinking the email is nonsense, she changes her mind when it begins playing a song that she recognizes from her youth.

Upon first meeting each other in person, the two are suddenly ambushed by gun-wielding men. While Mireille is capable of fending off the assault, she discovers that Kirika is quite adept in combat situations after she takes out several gunmen on her own. Despite her proficiency at killing, Kirika laments her inability to feel remorse for her victims. In addition, Kirika apparently has no memory of how she came to acquire the skills she possesses or even of her real identity.

Sensing shared history between them, Mireille agrees to team up with Kirika, and together, they embark on a journey to uncover the mysteries of their pasts. Operating under the codename "Noir," the duo's fragile alliance is tested as they begin accepting jobs, each one bringing them closer to the truth of who they really are.

Noir is the first original anime by director Kouichi Mashimo and studio Bee Train, which focused on the "Girls with Guns" sub-genre. It was later followed by two spiritual successors: Madlax in 2004 and El Cazador de la Bruja in 2007. Together, they are considered to be a Girls with Guns trilogy, even though the three TV series are unrelated story-wise.

A live-action adaptation of the anime series produced by TV network Starz was planned to release in the summer of 2012. But following a two-year hiatus starting in March 2012, the project was canceled in January 2014.