009 Re:Cyborg follows a group of nine cyborgs, each of them created by a shadowy organization for use as weapons against humanity. The group turns on their creators to protect the population instead, using the powers given them to fight their creators.

In Karakura Town, unidentifiable spirits begin appearing en mases. While attempting to deal with these strange souls, Ichigo Kurosaki and Rukia Kuchiki meet Senna, a mysterious shinigami who wipes out most of them. Senna refuses to answer any questions, so Ichigo is forced to follow her while Rukia tries to find out what’s going on.

Following Madoka’s rewriting of the universe, sacrificing herself and her happy normal days to save all magical girls from the cruel fate that awaited them by wiping witches out of existence, the despair still manifest into creatures known as nightmares. Magical girl Homura Akemi continues to fight alone in the hope that she will be able to see Madoka smile again.