Fujimiya Momiji is a descendant of the Kushinada clan, whose women possess the power to defeat the Aragami, an alien plant-like race, by sacrifice. After centuries of slumber, the Aragami have awakened and are invading Tokyo en route to conquering the world. In their way are the hapless schoolgirl Momiji, who becomes infected with one of the "Blue Seeds" –magatama beads that are the heart and soul of the Aragami, the TAC, a government agency whose sole mission is to stop the Aragami, and Kusanagi Mamoru, a young man infused with Aragami blood who swears vengeance on those who took his family away from him. Like the heroes of the past, this ragtag band of misfits must work together to defeat an ancient menace from the past, and one far closer to home.

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