The year is 2062. Earth has been left in ruin after the failure of a labor automation project when the AI called Artemis waged war against humanity. A girl, Empress, awakens in a research lab. As one of the three surviving guardians, she must destroy the Orbital Elevator before Artemis can complete its construction. Failure will result in a machine army overrunning Earth.

On the first day of junior high school, Mato Kuroi happens to run into Yomi Takanashi, a shy, withdrawn girl whom she immediately takes an interest in. Mato tries her best to make conversation with Yomi, wanting to befriend her. At first, she is avoided, but the ice breaks when Yomi happens to notice a decorative blue bird attached to Mato's phone, which is from the book "Li'l Birds At Play." Discovering they have a common interest, the two form a strong friendship. In an alternate universe, the young girls exist as parallel beings, Mato as Black★Rock Shooter, and Yomi as Dead Master. Somehow, what happens in one world seems to have an effect on the other, and unaware of this fact, the girls unknowingly become entangled by the threads of fate.

The story of two girls bound in friendship, as well as Black Rock Star's struggle unfolding in another world. But when the two worlds come together... what will happen?