The story begins with Orihime Shiki, a seemingly ordinary high school student who finds himself the target of bullying after transferring to Seikimantsu Academy. This academy is notorious for its poor discipline, earning it the nickname "End of the Century Academy." Shiki, a kind but somewhat naive individual, is forced to run errands for a group of bullies led by Kawato, often under strict time limits.
During one such errand to fetch drinks, Shiki accidentally collides with a striking red-haired girl, Kohinata Karin, causing his purchased drinks to fly into the air. Karin, however, astonishingly catches all three cans with incredible skill, stacking them perfectly on her closed iron fan. Shiki is awestruck by her prowess and her imposing presence. Karin, known as the "Empress" for her dominance within the academy, is revealed to be a formidable fighter who has subdued many of the school's delinquents. Despite her fearsome reputation, Shiki knows she is not a bully but rather someone who helps the weak. However, his fear of her strength prevents him from seeking her direct help.
Shiki returns to his classroom and is subsequently beaten by Kawato and his cronies for being late. They mock him, but Kawato reveals they hold back to avoid attracting Karin's attention. Shiki reflects on how his inherent kindness, which led him to help an elderly woman and a lost child on his entrance exam days, ultimately resulted in his current predicament. He had intervened when Kawato was bullying another student, which marked him as a target.
On a Sunday, Shiki attempts to enjoy a day off, but his plans are disrupted when he spots Kawato and his gang in town. He narrowly avoids them by hiding in an alley. While trying to escape, he witnesses Kawato forcibly dragging a beautiful, black-haired girl into the alley. Despite his fear, Shiki's sense of justice and compassion overrides his terror, and he charges at Kawato, allowing the girl to escape. Kawato, enraged, recognizes Shiki and, with his lackeys, drags him to a secluded parking lot for a brutal beating.
Just as the beating intensifies, Karin appears and swiftly incapacitates Kawato's henchmen. She then confronts Kawato, revealing that the girl he was harassing is her junior. Karin proposes a one-on-one fight between Shiki and Kawato, with her acting as Shiki's advisor. Shiki, though terrified, agrees. Karin's advice is unconventional: a powerful front kick to Kawato's abdomen. To his surprise, Shiki's kick, amplified by his desperation and the strength gained from his constant errands, incapacitates Kawato.
Karin explains that while Kawato and his gang are used to fighting, they lack true combat experience and are easily defeated by someone with genuine strength and determination, like Shiki. She then reveals her intention to teach Shiki how to fight, a proposition he accepts.
Later, Shiki, Karin, and Karin's junior, Momozono Haruno, meet in a secret "spare parts room" within the school, which serves as a hidden training area. Haruno, a clumsy but kind girl with medical knowledge, tends to Shiki's injuries. Shiki learns that Haruno was inspired to attend the academy after Karin saved her from a similar situation. During their training session, Shiki accidentally touches Karin's chest, leading to an embarrassing but ultimately humorous moment.
The narrative then shifts to Shiki's return to school. He notices he's being watched, and Kawato, despite Karin's intervention, still harbors resentment. However, Karin's presence seems to deter Kawato and his gang from directly confronting Shiki. During lunch, Shiki joins Karin, Haruno, and two other members of Karin's faction, Touka Hiyama and Chiaki Tsukiike, in the secret room. They discuss Shiki's decision to learn fighting and the dynamics of their group.
The chapters conclude with Shiki beginning his combat training under Karin's guidance, while the underlying tensions of the academy and the presence of other powerful factions, like the Arai faction led by Arai Ryogo, loom in the background. Shiki's life at Seikimantsu Academy is far from over, and his newfound connections promise to shape his future within this chaotic environment.