Mireille Bouquet is a professional assassin, and a very good one at that. But when she follows up an E-mail from a young Japanese girl named Kirika Yumura, inviting her to take "a pilgrimage to the past", her life becomes even more dangerous than it already was.

Now, with a haunting melody invoking the memory of an event long past, Mireille and Kirika decide to work together to find the truth about a thousand-year-old organization that has controlled both of their lives since before they were born. The only clue in their search, the only thing Kirika remembers about herself, becomes their working codename: a name designating an ancient fate, of two maidens who reign over death—Noir. 

After a mysterious earthquake levels Tokyo, Genom becomes a powerful influence providing their artificial organic lifeforms called Boomers to rebuild and act as a labor class to humanity.

However, some of them occasionally run amok, and even the specially created AD Police are at a loss to stop them. Lina Yamazaki travels to Tokyo for employment but also hopes to join a vigilante force called the Knight Sabers, who pilot powered suits to destroy these rogue Boomers. 

A mysterious reiatsu (spiritual particle) explosion occurs in the center of Seireitei in Soul Society, causing it to be destroyed. At the exact same time, a major change overwhelms Rukia Kuchiki, which leaves her losing something important inside. Kisuke Urahara sends Ichigo Kurosaki to Soul Society to investigate the disturbance. Upon reaching Seireitei, Ichigo is set upon and attacked by shinigamis, once allies, who have no memory of him and Rukia. Now alone and on the run, Ichigo must find the missing Rukia and uncover the cause of the mysterious incident before it's too late.