Gekkan Mousou Kagaku is set in Most City in an unknown country in a small publishing house that prints a monthly magazine about the most outlandish of things. Everything changes when the staff of the magazine, editor-in-chief Tarou, his assistant Jirou and dog Saburou, meet with scientist Gorou Satou...

Hiiragi Utena has always looked up to magical girls and fantasized about transforming into a cool heroine who fights evil. So, when a doll-like figure approaches her one evening, claiming that she has magical power lying dormant within, she trembles in excitement. But her colorful dream is quickly shattered in an ironic turn of events when she transforms into a villain! Disinterested in associating with the forces of evil, she tries to quit when a group of magical girls appear and declare war. A battle ensues and Hiiragi soon discovers that she enjoys inflicting pain on others as her true nature starts to emerge. Mahou Shoujo ni Akogarete follows Hiiragi as she begins her new life as the leader of villains, fighting against magical girls and indulging in her newfound sadistic nature to her heart's content.

When mundane office worker Kiyoshi Adachi turns 30 years old, he discovers that he has gained the ability to read minds due simply to remaining a virgin for his entire life. The caveat, however, is that he must make physical contact with a person to know what they are thinking about. Adachi believes there is no real use for this power until he accidentally hears the thoughts of his coworker, Yuuichi Kurosawa. Charismatic and dependable, Kurosawa is the star of Adachi's team at work, earning praise and admiration from everyone at the office. But deep within, Kurosawa harbors an intense one-sided crush for the gloomy Adachi—a fact that Adachi only learns because of his ability, and knowledge he tries to respectfully disregard. As Kurosawa treats Adachi with kindness and affection he has never experienced before, Adachi finds it increasingly difficult to ignore his coworker's genuine advances.

A team of three magical girls known as Tres Magia protects the town where Utena Hiiragi lives. Like many others, Utena loves these magical girls who valiantly fight in the name of justice. One day, a mysterious black mascot character appears before Utena and grants her the opportunity of a lifetime: a chance to transform into a magical girl. However, the offer is not what it seems, as Utena has been recruited for an evil organization to fight the magical girls she has always admired. Utena is then forced to confront Tres Magia in battle; but instead of feeling remorse, she unexpectedly finds pleasure in inflicting pain on the magical girls. Completely giving in to her desires, Utena embraces her role as a villain, slowly transforming her adoration for magical girls into a new sadistic obsession.