Sonnet is a cyborg/esper from a harsh background and now trained to be the ultimate warrior and most powerful weapon in the world. She is sent to Japan to watch Komatsuzaki Lan, who is thought to be controlled by the rage of the esper Akai Kiba (Crimson Fang). Lan is a quiet girl who knows she's different from everybody else and starts to show signs of Crimson Fang after coming into contact with Sonnet. In the course of fighting with Lan, Sonnet starts to rediscover her humanity. At the same time Lan has to fight to retain her humanity and control the Crimson Fang.

The warriors who have been warped by the rampaging power of Justice have been summoned into the world of Xanadu. It is up to Dark Fact, a former villain, and principal Lappi to re-educate these students.

CG short specials of Flying Witch posted on the official YouTube channel of distributor VAP and later bundled with the Blu-ray and DVD volumes.