In a near future, an illness called Cagaster made ​​its appearance. It turns humans into insects. The story begins 30 years after the onset of the illness, in 2125. It follows the adventures of Kidou, a boy who fights insects. (Source: MAL News)

Deep in the Ararat Mountains of Turkey, a secret organization known as ARCAM has found what is believed to be Noah's Ark. However, the U.S. Machine Corps., a rogue organization of the Pentagon, wants to take over the Ark as a means of global supremacy. Only a special ARCAM operative known as a Spriggan stands in their way. Japanese Spriggan Yu Ominae teams up with French Spriggan Jean-Jacques Mondo to combat members of the U.S. Machine Corps. led by Col. MacDougall—a genetically-enhanced boy with deadly psionic powers. However, they must act fast and stop MacDougall before he uses the Ark for his own agenda. (Source: ANN)

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?

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.