Kuroi Mato just got into junior high school, and on the first day, someone catches her eye; her classmate Takanashi Yomi. The two meet. The innocent and naive Mato and the mature Yomi. Seemingly opposites, but the time they spend together only strengthens a growing friendship. But as they go into their second year at the school, they get placed in separate classes, and they begin to grow apart.
But somewhere simultaneously… In another world, a young girl, blue fire residing in her eyes, Black Rock Shooter faces another young girl; this one holding a jet-black scythe, Dead Master, and a battle to the death begins to unfold.