Ten years ago, a volcanic eruption brought Japan's Ayaka Islands to the brink of destruction. Since then, Yukito Yanagi has lived with foster families on the mainland, but he has isolated himself from others following a disturbing incident. Due to the wishes of his late father, Makoto, Yukito is brought back to his birthplace on the day of his middle school graduation. There he meets Makoto's disciples and learns of the supernatural state of the region. Mysterious life forms known as Mitama inhabit the islands, but their potential to feed off humans' negative energy and turn into ferocious monsters called Ara-Mitama endangers the islanders' lives.

Yukito discovers that, like his father, he is a Ley Master—a special individual with abilities akin to magic, tasked with pacifying the Ara-Mitama. As he learns to overcome his trauma and control his powers, Yukito decides to follow in his father's footsteps and become a first-rate Ley Master to protect the peace of Ayaka.