The Inquisition is the primary faction that represents most of the "normal" humans in the series. It was formed from before the first great war and it persecuted any and all magic-users and branded them as "loathsome" and "heretical". Since normal humans couldn't possibly face a magic-user, the Inquisition was formed to train regular people into being able to fight back against the threat. The Inquisition was created and is led by Sougetsu Ootori, where he presides as its supreme authority. Beneath him are the militant troops that act as peacekeepers and protect the public from magical threats. The Inquisition's military is separated into distinct branches:

  • Spriggans are the general combat troops that make up the bulk of the Inquisition's fighting power.
  • Banshees are specialized agents that focus on operations involving stealth and intelligence gathering.
  • Seelies are the combat medics that assists those under magic-related damages.
  • Reginnes are the technological experts that develop, maintain, and research anti-magical equipment.
  • Dullahans are exceptionally talented, independent agents that are allowed to pursue and investigate their own cases and mete out injustices. A special police squad known as the EXE is exclusively comprised of Dullahans

The Anti-Magic Academy was constructed after the war to serve as a training grounds for youths to learn about the "heretical" practices of magic and ways to fight back. As they graduate after attaining points from their assignments, they are inducted into one of the five branches of the Inquisition.