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In the year 2062, Earth finds itself fiercely battling Artemis—an AI which rebelled against humankind following a grand-scale workforce automation project failure years prior. In the hope of winning the war, a group of three highly skilled human warriors is assembled, known as the guardians of humanity. Empress, the last surviving guardian, wakes up alone in an empty research facility. Unable to recall anything from the past except a place called "Lighthouse No. 8," she begins to search for answers. It is not long before she discovers an impending threat from Artemis—and she is the sole person who can save the world from destruction.

On the first day of junior high school, Mato Kuroi happens to run into Yomi Takanashi, a shy, withdrawn girl whom she immediately takes an interest in.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. [Written by MAL Rewrite]