In another world, the eponymous Black Rock Shooter battles a mysterious red-eyed opponent. Meanwhile, in the human world, Mato Kuroi enters middle school and takes an interest in her classmate, Yomi Takanashi. The two quickly become friends due to their common fondness for a book from their childhood. After inviting Mato to her house, Yomi becomes worried when Kagari Izuriha, a wheelchair-bound girl who wants to keep Yomi to herself, arrives and acts with hostility towards Mato, causing her to become frightened. Meanwhile, in the other world, Black Rock Shooter follows a green trail to a wasteland filled with broken toys where she is attacked by a girl resembling Kagari named Chariot.

As Black Rock Shooter continues to struggle against Chariot and Dead Master, Mato waits at the festival for Yomi, but she never arrives as Kagari wouldn't let her. As Mato dreams that night of Black Rock Shooter, who had a heart scarred on her chest, she discovers Yomi has the same scar the next day, yelling at her for having no spine. After consulting with Saya, who tells her dreams serve a deep meaning between friends, Mato goes to Yomi's house, but Kagari stops Yomi from coming to see her by throwing herself down the stairs. As Kagari is taking into hospital for a twisted wrist, Mato hears from Yomi's mother about how Kagari was hit by a car whilst chasing after Yomi, demanding she look after her. Determined in her belief that Yomi shouldn't suffer for that, Mato voices her pleas to go home with Yomi, calling her by her first name. Mato helps Yomi realise her true feelings, wanting to be earnest friends with both Mato and Kagari. As Dead Master manages to break free from her binds, but she is captured by another evil, Black Gold Saw, whilst Black Rock Shooter is forced to kill Chariot, which has its effect on Kagari.

As Mato prepares to go to training camp with her basketball club, Yomi starts to become jealous of Mato's childhood friend, Yuu Kotari. Mato has more dreams involving Black Gold Saw during camp, and at the same time, Saya takes an interest in Yomi. Upon returning to school, the basketball coach, Arata Kohata, discovers the boy she had a crush on had posted her love letter for all to see. She holds back tears in front of the crowd, and ultimately laughs off the incident as if it hardly mattered to her. Kohata visits Saya afterward, but Saya begins acting strangely by taunting Kohata, reminding her that everyone is laughing at her. In the other world, Black Rock Shooter attacks Black Gold Saw's hideout, killing her minions. Simultaneously in the human word, Kohata experiences a sudden pain in her head and falls unconscious in front of Mato.

In the other world, another being named Strength is seen throwing Chariot's corpse off a cliff. Meanwhile, Kagari starts going to school and starts making friends which, on top of Mato's duties with her club, causes Yomi to feel unwanted. As Kagari asks Mato for some advice on how to cheer up Yomi, they stumble upon Yomi arguing with Kagari's friends, saying something she soon regrets and locking herself in her room, ignoring Kagari's visits. The next day, the boy Arata confessed to the other day tries to apologise to her, but she has no memory of him. Meanwhile, Yomi falls further into depression when she receives a text from Yuu. Believing Kagari to be the only one who would need her, Yomi snaps when Kagari tells her to let her go. This has an effect on the other world, as Dead Master emerges with a darker personality and stands off against Black Rock Shooter.

As Black Rock Shooter fights against a huge army under Dead Master's control, Yomi behaves strangely at school, cutting her hair in class, causing Mato to become concerned, even lashing out at Kagari. As Yuu becomes cautious of Saya's actions, Mato sees the battle between Black Rock Shooter and Dead Master in her sleep. As Mato visits Saya the next day, she tries to strangle her, leaving her confounded. After seeing the painting Yomi drew of her, Mato comes to realise that is because of her that Yomi is suffering. She soon discovers that noone in the basketball club remembers Yuu, soon finding her own memories of her to be a lie. Yuu then appears before her, telling her that the other world in her dreams is real. She explains how the people in the other world represent the sorrow upon their real world counterparts, and if they are killed, the person forgets about their attachments that caused them that grief, meaning if Dead Master is killed, Yomi would forget all about her. Offering Mato the chance to save Yomi without resorting to fighting, Yuu puts her into a deep sleep, sending her mind into that of Black Rock Shooter, only to find she had just killed Dead Master. The shock of this causes Black Rock Shooter's blazing blue eye to become purple, becoming Insane Black Rock Shooter.

As Mato breaks down from what she had just done, Black Rock Shooter transforms into Insane Black Rock Shooter and stands against Black Gold Saw. As Black Rock Shooter rips off her own arm to fight against Black Gold Saw, Mato passes out from the pain, preventing Yuu from calling her back to her body. She brings her to Saya, who wanted to prevent Black Rock Shooter from causing destruction in the other world, but can't bring herself to kill Mato in order to do so. Instead, Saya transport her mind to Black Gold Saw's so she can try to reach Mato. Saya talks about how she befriended Yuu, who had been constantly bullied at both home and school. One night, when Yuu's house caught fire, Saya wrongly assumed Yuu was responsible and felt guilty. When Saya found her the next day, she asked Saya to protect her and awakened her connection to Black Gold Saw. Back in the present, Strength steps in to fight Black Rock Shooter in Black Gold Saw's place, allowing Saya to return. As Strength overwhelms Black Rock Shooter in battle, Yomi returns to school with no apparent memory of Mato.