On her first day of junior high school, Mato Kuroi meets Yomi Takanashi. Though Yomi is initially taken aback by Mato's straightforward personality, the pair quickly becomes friends and begin to spend time together daily. As a sign of their friendship, Mato gives Yomi a cell phone charm—a blue star, identical to her own.

However, when the two enter their second year, their relationship starts to change. Placed in a different class, Mato begins to spend more time with Yuu Koutari instead, a girl she met through the basketball team. In fact, the former best friends drift apart so much so that Mato cannot find Yomi anywhere, as if she had disappeared entirely.

Elsewhere, Black★Rock Shooter is on a quest to vanquish the Dead Master. These two, while opposed, bear a connection not unlike Mato and Yomi. As their stories begin to cross, it seems Yomi's disappearance may have to do with the blue star-shaped charm and the legendary gunslinger herself.