Many years prior to the anime's beginning, presumably sometime around Mato Kuroi's birth, she appeared in the Otherworld as a manifestation of Mato's desire to help people while ignoring her own pain. This desire gave her a large amount of physical ability.

She fought Strength on a ledge, and while neither had the ability to feel emotions, Strength could sense that Black★Rock Shooter was exceptionally powerful; they fought, and Strength was defeated.

At the start of the anime, Black★Rock Shooter is at the Sky Gates. After walking around, she comes upon some green mist, and is led into a strange area where she is tormented by mysterious spider-like robotic creatures and Chariot. At one point, she screams silently in pain as one of the robots stabs and drills into her stomach.

She is then accosted by Dead Master and is chained up, but she quickly reverses the chains. However, a horde of spiders surrounds Dead Master and carries her away, causing Black★Rock Shooter to pursue her.

She finds her in a floating house in the sky, hidden within a doll and chained up. She reaches for her but is stopped by Chariot and her spider robot. The robot begins to fire macaroons (a motif associated with Chariot's other self) at her, but she takes out her gun and shoots at them; the robot fires a torrent of macaroons at her, and she upgrades her gun to a machine gun-like contraption that blows them all away and destroys the spider robot.

During that time Dead Master begins to break free from her chains, and Black★Rock Shooter gains the upper hand. The chains recede into the sky, causing the world to fall apart. However, this is driven to a halt as a large red blade is driven into the sky, stopping this and suspending the destruction in midair, as if time had been stopped for the destruction. She and Dead Master find Black★Gold Saw with Chariot.

Black★Gold Saw cuts a fissure into the ground, dragging Dead Master into it and apart from Black★Rock Shooter, and vanishes. Chariot takes the opportunity to charge at Black★Rock Shooter with her blade, but Black★Rock Shooter quickly ignites the blue flame on her eye and beheads Chariot.

Later, she breaks into Black★Gold Saw's lair, and causes rocks to fall onto the mysterious hooded figures that she has created. She shoots at Black★Gold Saw, who dodges and presumably escapes. She approaches one of the hooded figures, which resembles Arata Kohata, and holds a hand out to her. However, the figure recedes and trembles in fear, and in response, she ignites her flame, grabs the figure, and beheads it.

When Dead Master starts to become unstable, she goes to investigate. When Dead Master summons a castle and minions, she attempts to shoot her but is hit by one of Dead Master's floating skulls and hits a wall. She then readies her gun and fires at Dead Master.

At the climax of the battle, Mato Kuroi merges with her in order to save Black★Rock Shooter; however Black★Rock Shooter has already killed Dead Master by the time she arrives sending Mato into shock. The shock of having killed Yomi's "other self" causes Black★Rock Shooter to become unstable and combine red flames into the blue flames around her eye, creating a large amounts of purple flame. A red light appears in her pupils and she seems to go insane, transforming into Insane Black★Rock Shooter. In this form, B★RS goes on a deadly rampage until defeated by Mato (in B★RS's normal form), with the help of the revived other selves. Following the battle, she reverts back to normal.

She next appears on a cliff as Strength tells Yuu that the other selves fight because they love and wish to protect their real world counterparts, echoing the sentiment to Mato. After Strength's death, she jumps off the cliff, her words echoing to Mato as she leaves the Otherworld.

She later appears on a cliff in front of the reformed Strength, stating that she won't stop fighting or bearing the pain in the Otherworld.