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.

Tatara Fujita is a shy middle schooler who has no particular plan for the future. He has gotten through life by avoiding any kind of confrontation and blending in with the crowd. But blending in isn't enough to get out of trouble, as some bullies harass him for money. Luckily, he is saved by a man named Kaname Sengoku. Kaname invites Tatara to his dance studio. Although he would normally never set foot in such a place, Tatara is captivated by Sengoku's commanding presence. Granted an opportunity to dance with fellow classmate Shizuku Hanaoka—who often practices at the studio—Tatara realizes there's something about the idea of being put in the limelight and dancing where people will see him that keeps him coming back. With an earnest, passionate drive to improve, Tatara begins his journey into the world of competitive dance.