"The Qwaser of Stigmata" is a supernatural action manga set in a world where certain individuals, known as Qwasers, wield divine powers derived from the manipulation of chemical elements. These powers are fueled by Soma, a sacred substance obtained through intimate interactions, often involving the breasts of female characters. The story centers around the conflict between the Orthodox Church and the Athos religious organization, which seeks to harness the power of the Theotokos of Tsarytsin, a powerful relic with immense destructive potential.

The protagonist, Alexander "Sasha" Nikolaevich Hell, is a silver-haired Qwaser who wields the power of iron. Sasha is a stoic and determined fighter, driven by a personal vendetta against those who wronged him in the past. He arrives at St. Mikhailov Academy, a school with ties to the Athos organization, where he encounters Mafuyu Oribe, a kind-hearted but strong-willed girl who becomes a key figure in the unfolding events. Mafuyu’s younger sister, Tomo, is revealed to be the vessel for the Theotokos of Tsarytsin, making her a target for both the Athos and Orthodox factions.

As the story progresses, Sasha forms alliances with other Qwasers and students at the academy, each possessing unique elemental abilities. These include Hana Katsuragi, a Qwaser who controls hydrogen, and Miyuri Tsujidou, a skilled fighter with a deep connection to the Orthodox Church. The narrative explores themes of faith, sacrifice, and the moral complexities of wielding divine power, as the characters navigate a web of conspiracies, betrayals, and battles.

The conflict escalates as the Athos organization, led by the enigmatic and ruthless Aoi, seeks to use the Theotokos of Tsarytsin to achieve their goals, while the Orthodox Church strives to prevent its misuse. The story delves into the origins of the Qwasers, their connection to the Virgin Mary, and the tragic histories that shape their motivations. The battles between Qwasers are intense and strategic, often involving intricate uses of their elemental powers and the vulnerabilities tied to their reliance on Soma.

Throughout the series, the characters face personal struggles and moral dilemmas, with Sasha’s journey of redemption and Mafuyu’s determination to protect her sister serving as central emotional arcs. The narrative balances action-packed sequences with moments of introspection, exploring the psychological and emotional toll of the characters’ roles in the larger conflict. The manga concludes with a climactic confrontation that resolves the central conflict while leaving room for reflection on the consequences of the characters’ actions.