The Heretic Alliance is a union of three factions that are made of the dissident members from the Inquisition, the Magic Academy, and outer factions, brought together under the belief that their leaders are working toward an ultimately destructive goal that threatens the world. It was "led" by Nagaru Hoshijiro and joined by the 35th Test Platoon as well as a number of Inquisition members including ex-EXE operative, Oonogi Kanata. The other two sides are represented by Sage from the Magic Academy and Mikado Yuzuho from the God's Embers, an organization consisting of the remaining world's religious groups.

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