In a surreal world of abundant wonders, Gil is a workshop town specialized in mechanical craftsmanship, boasting the largest population in the land of Piril. People lead simple lives with little to no advancement in technology, worshipping Marie, a mechanical Goddess who keeps vigil of Piril from the sky.

Daughter of the top mechanical artisan of Gil, Pipi is a cheerful and popular young girl. She likes her childhood friend, Kai, who has an extraordinary ability to hear sounds inaudible to the human ear. He is the only one in town who can listen to Marie's "music." The soothing sounds that come from her are said to retain the peace and harmony of the land. Kai's affection for Marie deepens as he continues to experience these sounds and see visions of himself through her eyes.

Exploring the fantasy world of Kai and Pipi, Marie no Kanaderu Ongaku tackles concepts of religion, technology, and what it truly means to be happy.