Kindergarten Noir is widely known as the world's safest kindergarten. Its students are exclusively the children of the world's most powerful politicians, celebrities, and business moguls, making them constant targets for assassins and kidnappers. The school's security is guaranteed not by ordinary guards, but by its teaching staff, who are all convicted criminals working to reduce their sentences. The plot follows Rita, a 20-year-old former legendary assassin known as Convict #999 and nicknamed The Witch, who takes a job at this institution. While her official duties are to teach and protect the children, her personal goal is far less noble: to find a handsome boyfriend among the endless stream of attackers.

The series combines violent action with romantic comedy as Rita effortlessly defeats most threats with her superhuman strength and mastery of all weapons. Her critical weakness, however, is that she falls head-over-heels for any good-looking man she encounters, even when that man is an assassin trying to kill her students. She has developed a personal rule that if a handsome killer shares her romantic tastes, she might spare his life, but if his answers displease her, she shoots him without hesitation. This running gag defines much of the early conflict as Rita navigates her contradictory desires for love and survival.

Rita works alongside a colorful cast of fellow former criminals in the Dandelion Class. Her colleague Doug is a 23-year-old American former con artist and self-described womanizer who develops genuine feelings for Rita. Despite his past as a swindler, Doug possesses sharp observational skills, a near-photographic memory for the children's faces, and surprising competence. Later, Hana Bradley, an 18-year-old from a notorious assassin family, joins the staff as a junior teacher, wielding a baseball bat combined with explosives. The faculty also includes the Chrysanthemum Class teachers Luke Smith, a stoic former police officer who murdered his superior and now secretly loves shojo manga, and his partner Silvia, a former smuggler who quietly harbors feelings for Luke. Overseeing them all is the stern former soldier and园长 Erina, who tracks every teacher with GPS chips and allows them no freedom outside school grounds unless actively protecting students, alongside the bear-like but peace-loving副园长 and school doctor Gordon Z. Sky.

A significant narrative arc involves Hana temporarily betraying the kindergarten to rescue her brother Shaw from their criminal family, an incident that strengthens her bond with the team and leads to her full acceptance. Another major thread introduces the跨国犯罪组织 New World Order, led by Leo, who is revealed to be Rita's twin brother. Leo orchestrates attacks targeting a mysterious and critically important student named Lyla, suggesting that the kindergarten's true purpose may extend beyond mere protection. The series gradually hints at deeper conspiracies, as Doug grows suspicious of the园长's true motives for assembling such a dangerous group of convicted killers.

As the story progresses, a romantic relationship slowly develops between Rita and Doug, much to the delight of Luke, who views their love triangle with Hana as real-life shojo manga drama. The manga has been collected into multiple volumes, and an anime television series adaptation has been announced, bringing this story of the world's most dangerous preschool to the screen.