A nameless Sage created the world and stabilized reality centuries ago by forging 6 elemental Cores. When the Cores scattered across Japan, 70% of humanity was granted the ability to use Magic.

Today, everything is powered by magic: airships, city lights, etc. However, when mana mutates or overloads, it takes the form of hideous beings known as Mares.

17-year-old Sora Minami, one of the 30%, leads a peaceful, unremarkable life. Until an unexpected mass outbreak of Mares turned streets into chaos. In the midst of the disaster, he discovers an ancient weapon in an abandoned shrine that pulses with light: the Genesis Engine.

It grants him the power of the 6 Cores, allowing Sora to transform into the Genesis Knight! His awakening draws the attention of the Mana Hazard Response Agency, a secret government organization that manages Mare's incidents.

With new allies, Sora sets out to collect all 6 cores. But each battle brings him closer to the truth of this world.