The story begins with the protagonist, Kisaragi Kurona, reflecting on his past decision to become a magical girl, driven by a desire to please his beloved younger sister, Karen. While initially proud of his choice, he now harbors regrets, finding the path more difficult than anticipated.
The narrative then shifts to a typical morning. Kurona is awakened by his alarm clock, only to find it missing. His sister, Karen, enters his room, revealing she took it and urging him to come down for breakfast. Karen is depicted as a beautiful, somewhat aloof girl, with sharp eyes and long black hair, possessing an air of a noble lady. Kurona notes her usual cold demeanor, which paradoxically adds to her charm. He wonders why she bothered to wake him, as she normally wouldn't.
He soon remembers that today is Karen's high school entrance ceremony, and as their parents are abroad, he is expected to attend as a guardian. The school is closed for regular students, with only new students and their guardians attending. Kurona reflects on his parents' absence and his own feelings about it.
During breakfast, Karen is impatient, and after eating, she announces she's leaving, refusing to walk to school with Kurona, citing the need for guardians to arrive later. After she leaves, a small, peculiar creature named Mepol, who can speak, appears. Mepol is Kurona's contract spirit and the source of his magical girl abilities. Kurona is accustomed to Mepol's presence and their conversations.
While eating, Kurona watches the news and hears about a phantom that was defeated by an unknown hero. This leads to an explanation of phantoms: beings from the dark world who feed on negative emotions. They don't just take negative emotions; they also take the corresponding positive emotions, leaving victims emotionally unbalanced. Humans and phantoms are thus enemies. Initially, police and military were ineffective against phantoms, but then "heroes" emerged, empowered by positive emotions. These heroes are known by various names, including "magical girls."
Mepol alerts Kurona to a phantom nearby. Kurona realizes he's running late for Karen's ceremony but cannot ignore the phantom. He decides to quickly deal with it. Despite his reluctance, he transforms into his magical girl persona, Magical Flower Black Rose. His transformation is described in detail: his school uniform disappears, replaced by a black, gothic lolita-style outfit with ribbons, his hair lengthens, and his body becomes more feminine. He expresses his deep regret at being a male magical girl, a secret he cannot easily reveal.
Kurona quickly defeats the phantom, a goat-like creature, and then encounters a student from his own high school, a freshman named Amasaki Sakura, whom he had previously rescued. Realizing she is also late for the ceremony, he offers to escort her. He carries her to school in a princess carry, a decision he makes to avoid being late himself and to maintain his secret identity. During the flight, he is unaware of being watched with malicious intent.
Upon arriving at the school, Kurona, as Black Rose, explains the situation to a teacher, Ayame Nanri, who is surprised but grateful. Nanri invites Black Rose to participate in the entrance ceremony as a guest, which Sakura enthusiastically supports. Kurona agrees, seeing it as a way to attend the ceremony without revealing his identity as Kisaragi Kurona. He attends the ceremony in his magical girl attire, feeling out of place but also receiving positive attention from the students. He notices Karen looking troubled and searching behind her.
After the ceremony, Kurona returns home, expecting Karen to be angry about his tardiness. However, Karen is surprisingly calm, though distant. She questions his presence at the ceremony, and Kurona, unable to lie convincingly, admits he attended as Black Rose. This leads to an argument where Karen expresses her hurt and anger over his absence at her actual entrance ceremony, accusing him of only wanting to appease her. Kurona is devastated by her words.
The next day, Kurona is still upset and seeks advice from his childhood friend and fellow hero, Izumi Mikuru (Crimson Flare). Mikuru suggests they consult with Asami Midori, another childhood friend, who is known for her insight into girls' emotions. They go to Midori's classroom, where Kurona is awkwardly embraced by Midori, who has a possessive streak towards him. Midori, along with her friends Miki and Saki, agrees to help. Midori devises a plan: Kurona, Karen, and Sakura will go shopping together, with Sakura acting as a facilitator.
During the shopping trip, Kurona is forced to wear women's clothing, much to his embarrassment, after a store manager and the girls insist he model for a poster. He endures this ordeal, hoping it will help mend things with Karen. Later, while waiting for Karen to use the restroom, Sakura reveals that Karen had confided in her about being upset with Kurona. This gives Kurona hope.
As Kurona is about to apologize to Karen, a powerful phantom named Tsige appears, targeting Sakura because she has the potential to become a magical girl. Tsige reveals that he is targeting Sakura to prevent her from becoming a threat and that he is also interested in Black Rose's energy. Tsige's two goat-like subordinates, whom Kurona had previously defeated, appear. Tsige offers Kurona a chance to escape alone, but Kurona refuses.
Just as Tsige is about to attack, Sakura transforms into a magical girl, Magical Flower Cherry Blossom, using a pink gothic lolita outfit. She bravely confronts Tsige, while Kurona takes Karen to safety. Sakura fights Tsige, displaying immense power but also a lack of experience. She is eventually defeated and injured.
Kurona, seeing Sakura's struggle and Karen's distress, decides to reveal his identity as Black Rose to Karen. He transforms in front of her, explaining his actions and apologizing for missing her ceremony. To his surprise, Karen is not disgusted but proud of him for protecting others. She reveals she knew he was Black Rose all along and was upset not by his identity, but by his absence at her ceremony.
With Karen's acceptance, Kurona rushes back to help Sakura. He finds Sakura struggling against Tsige, who has revealed his true form. Tsige is immensely powerful, and Sakura is on the verge of defeat. Just as Tsige is about to deliver a finishing blow, a blinding light envelops the scene. When it clears, Sakura has transformed into a magical girl, and a new, powerful entity appears, seemingly related to Tsige. The story ends with the implication of a larger conflict and the emergence of new magical girls.
