The overarching narrative features several major revelations and climactic developments:
- Touma's Secret Amnesia: In saving Index from the Anglican Church's automatic defensive system (Walking Church / Feather of Light), Touma suffers brain trauma destroying his autobiographical memory. He conceals this truth from Index and his peers for the entire series to spare them guilt.
- The Nature of Academy City: Academy City is revealed not to be an educational haven, but a massive arcane ritual testing ground constructed by former occult master Aleister Crowley to orchestrate the demise of the magic world.
- The Right Seat of God Conspiracy: The Roman Catholic faction's core members (Vento, Terra, Acqua, and Fiamma) exploit ideological rifts to trigger World War III.
- World War III Climax: Fiamma summons the flying fortress Star of Bethlehem to seize Touma's right hand and Index's grimoires to summon Archangel Gabriel and recreate the world. Fiamma severs Touma's arm, but an unfathomable draconic energy surges from the stump, overpowering Fiamma before Touma regenerates Imagine Breaker. Accelerator decodes angel language to stabilize Last Order and manifests divine White Wings to halt a tactical explosion, while Hamazura secures safety for Takitsubo. Touma spares Fiamma and steers the fortress into the Arctic Ocean, where he is left behind and presumed dead.