Mahou Shoujo no Taisetsu na Koto.

The main character is an average student (except for his pretty appearance). He has moved to a school on the island to look for his missing mother. But an upside-down chapel that appears in the sky at night, evil shadows generated by the chapel and various mysterious happenings keep bugging people on the island. He inevitably gets involved in this trouble and he transforms into a magical girl (?) when he faces one of the shadows. Days later, he hears the fact that his mother is actually a magical girl. Like this, his battle life against the shadows starts...