Having fulfilled their destiny during the events of Yuuki Yuuna wa Yuusha de Aru, Sanshu Middle School's Hero Club—consisting of Yuuna Yuuki, Karin Miyoshi, and siblings Fuu and Itsuki Inubouzaki—is back in full swing, helping out those in need wherever they can. They have also gained a new member, a hero from the past named Sonoko Nogi. But eventually they notice that someone who should be among them, Mimori Tougou, is missing; any trace of her existence is completely gone, save for the girls' memories. With no leads on Tougou's whereabouts, the girls regain the ability to transform and begin the desperate search for their lost friend. But what they find is more shocking than any of them could ever have imagined, and the consequences of their actions begin to change life as they know it.

Three girls have been chosen by the great Shinju-sama to be heroes and fight against the destructive beings known as Vertexes—enemies that threaten the harmony and safety of the world. Unsure of when they would be called to duty, Sumi Washio, Sonoko Nogi, and Gin Minowa spent their time idly. However, with the sudden appearance of a Vertex, they realize they have no idea how to fight together as magical girls when they are nearly bested. They manage to defeat their enemy by sheer determination, but in the aftermath of the battle, the three decide to fix their teamwork issues and improve their combat capabilities. But as more enemies appear—and requiring even more power to defeat their nemeses—the girls may find themselves irreversibly changed by the use of their magic. What price will they have to pay to ensure victory, and is it one worth paying if humanity will be saved?

In her everyday life, Yuuna Yuuki is a hero. As proof, she is in her middle school's Hero Club, where she does her best to help others and bring a smile to everyone's face. But Yuuna, always up to any task, is about to become an even bigger hero. Mysterious destructive forces called Vertexes begin threatening the world she loves, and the Hero Club is called upon by a strange phone app to save it. Along with her best friend Mimori Tougou, as well as sisters Fuu and Itsuki Inubouzaki, they must transform into magical girls in order to battle the Vertexes. In between studying and putting on shows for kids, Yuuna and the Hero Club must fight for the very existence of their world and face the harsh truths behind their own powers, all the while discovering what it truly means to be a hero.

Dreaming of becoming a hero and vanquishing the Demon King, Raul Chaser enters the Hero Training Program in pursuit of his ambition. However, when the Demon King is defeated and peace returns to the world, the Hero Training Program is suspended indefinitely, making it impossible for anyone to become a hero. Two years later, Raul reluctantly works at a small electronics store called Magic Shop Leon. Though the former hero-in-training is plagued by the mundanity of working in retail, everything changes with the arrival of a new hire. Appearing at first to be just a boy with good looks, he turns out to be a female demon by the name of Fino Bloodstone. She is not just any old demon either—Raul's new coworker is in fact the daughter of the late Demon King! Handed the responsibility of training this eccentric new employee, Raul soon finds his life becoming livelier than it ever was before.