"Masō Gakuen H×H" is an anime series adapted from the light novel series written by Kuji Masamune. The story is set in a world where humanity faces threats from extradimensional beings known as "AHSMB" (Anti-Human Sentient Mobile Battle-fortresses). To combat these threats, humanity develops advanced hybrid weapons called "Hybrid Counters," which require a unique form of energy generated through intimate interactions between male and female users. The narrative centers on Kizuna Hida, a young man who becomes a key figure in the fight against AHSMB after being transported to an alternate world where the conflict is ongoing.

Kizuna is enrolled at Ataraxia Academy, a specialized institution training students to pilot Hybrid Counters. He is paired with Aine Chidorigafuchi, a skilled but initially reluctant partner. Their partnership is crucial, as the energy required to power their weapons, known as "Heart Hybrid," is generated through heightened emotional and physical intimacy. As the story progresses, Kizuna forms bonds with other female pilots, including Himekawa Hayuru and Yurishia Farandole, each of whom possesses unique abilities and personalities. These relationships deepen as they work together to protect their world from the AHSMB threat.

The plot explores the dynamics of teamwork, trust, and the ethical dilemmas surrounding the use of intimacy as a weapon. The characters face challenges not only from external enemies but also from internal conflicts and the moral implications of their actions. The series balances action sequences with character development, highlighting the emotional and psychological struggles of the pilots as they navigate their roles in the war. The narrative also delves into the origins of the AHSMB and the broader implications of the conflict for humanity's survival. Throughout the series, Kizuna and his allies strive to uncover the truth behind the AHSMB while strengthening their bonds to enhance their combat effectiveness.