"Battle Girl High School" is set in a world where humanity faces constant threats from mysterious alien creatures known as Irousu. These beings drain energy from the Earth, leaving destruction in their wake. To combat this threat, young girls with special abilities, called Hoshimori, are trained at Hinomori Girls' Academy. The academy serves as both a school and a training ground, where students learn to harness their powers and protect the planet.

The narrative centers on a group of students at Hinomori Girls' Academy, each possessing unique combat skills and weapons. The protagonist, Yui Tomita, is a transfer student who joins the academy and quickly becomes involved in the fight against the Irousu. Alongside her classmates, Yui forms bonds and trains rigorously to improve her abilities. The story explores the daily lives of these students as they balance their academic responsibilities with their duties as defenders of Earth.

Key characters include Asuka Harukawa, a skilled and determined leader; Kurumi Tokishima, a cheerful and energetic fighter; and Miki Hoshitsuki, a calm and analytical strategist. Each character brings distinct strengths and personalities to the group, contributing to their collective efforts in battling the Irousu. The series delves into their personal struggles, friendships, and growth as they face increasingly dangerous threats.

The plot progresses through episodic battles against the Irousu, interspersed with moments of camaraderie and school life. As the students grow stronger, they uncover more about the origins and motives of the Irousu, leading to larger confrontations and higher stakes. The series combines action, teamwork, and slice-of-life elements, creating a narrative that balances intense combat with the everyday challenges of being a student.