Cocona is an average middle schooler living with her grandmother. And she who has yet to decide a goal to strive for, soon met a strange girl named Papika who invites her to an organization called Flip Flap. Dragged along by the energetic stranger, Cocona finds herself in the world of Pure Illusion—a bizarre alternate dimension—helping Papika look for crystal shards. Upon completing their mission, Papika and Cocona are sent to yet another world in Pure Illusion. As a dangerous creature besets them, the girls use their crystals to transform into magical girls: Cocona into Pure Blade, and Papika into Pure Barrier. But as they try to defeat the creature before them, three others with powers from a rival organization enter the fray and slay the creature, taking with them a fragment left behind from its body. Afterward, the girls realize that to stand a chance against their rivals and the creatures in Pure Illusion, they must learn to work together and synchronize their feelings in order to transform more effectively.

An established discipline on par with conventional medical approaches, "vocal medicine" is the practice of using songs to treat health conditions and injuries. Young people around the world strive to master the art and become "healers" to help people through the power of their voices. Among the many healers in training is Kana Fujii, a naturally talented singer who was inspired to pursue the profession after a life-changing experience. Along with the driven Reimi Itsushiro and the easygoing Hibiki Morishima, Kana trains at Karasuma Phoniatric Clinic under the stern yet kind mentorship of Ria Karasuma. As they endeavor to achieve their dreams, Kana and her friends meet various colorful healers along the way, discovering that there is much more to vocal medicine than just diligent studying!

In the near future, humans have discovered a fourth dimension, Dimension W, and a supposedly infinite source of energy within. In order to harness this profound new energy, mankind develops advanced "coils," devices that link to and use the power of Dimension W. However, by year 2071, the New Tesla Energy corporation has monopolized the energy industry with coils, soon leading to the illegal distribution of unofficial coils that begin flooding the markets. Kyouma Mabuchi is an ex-soldier who is wary of all coil-based technology to the extent that he still drives a gas-powered car. Kyouma is a "Collector," individuals with the sole duty of hunting down illegal coils in exchange for money. What started out as just any other mission is turned on its head when he bumps in Mira Yurizaki, an android with a connection to the "father" of coils. When a series of strange events begin to take place, these two unlikely allies band together to uncover the mysteries of Dimension W.