"The Qwaser of Stigmata" is set in a world where certain individuals, known as Qwasers, possess supernatural abilities derived from the manipulation of chemical elements. These powers are fueled by Soma, a divine energy obtained through a unique method involving the consumption of breast milk. The story centers around the St. Mikhailov Academy, a prestigious school with a dark secret: it is a battleground for Qwasers who serve opposing factions in a hidden war over the Icon of the Theotokos, a sacred artifact with immense power.

The protagonist, Alexander "Sasha" Nikolaev, is a silver-haired Qwaser who wields the power of iron. He arrives at St. Mikhailov Academy under mysterious circumstances and becomes entangled in the conflict surrounding the Icon. Sasha is a stoic and determined individual, driven by a personal vendetta against the Athos Order, a rival faction seeking to exploit the Icon's power for their own purposes. His abilities are formidable, but his reliance on Soma creates a dependency that complicates his mission.

Mafuyu Oribe, a kind-hearted and strong-willed student at the academy, becomes a key figure in the story after encountering Sasha. She is revealed to be a "Maria," a rare individual capable of producing Soma, making her a target for both factions. Mafuyu's relationship with Sasha evolves as she becomes his primary source of Soma, and her protective nature often puts her at odds with the dangers surrounding the Qwaser conflict. Her younger sister, Tomo Yamanobe, also plays a significant role, as she harbors a mysterious connection to the Icon of the Theotokos.

The narrative explores the escalating tensions between the Qwasers of the Orthodox Church, who seek to protect the Icon, and the Athos Order, who aim to use its power for destructive purposes. The series delves into themes of faith, sacrifice, and the moral ambiguities of power, as characters grapple with their roles in the conflict. The battles between Qwasers are intense and often brutal, with each combatant utilizing their elemental abilities in creative and strategic ways.

Supporting characters, such as Hana Katsuragi, a skilled martial artist and ally to Sasha, and Miyuri Tsujidou, the academy's student council president with her own hidden agenda, add depth to the story. The series also introduces a range of antagonists, including the enigmatic and ruthless Qwasers of the Athos Order, who challenge Sasha and his allies at every turn.

As the story progresses, the true nature of the Icon of the Theotokos is gradually revealed, along with its connection to the origins of the Qwasers and their powers. The stakes rise as the conflict intensifies, leading to dramatic confrontations and revelations that test the resolve of the characters. "The Qwaser of Stigmata" combines elements of action, supernatural intrigue, and philosophical undertones, creating a narrative that is both complex and engaging.