From her hometown to her daily life on Kurken Island, everything surrounding Reisalin "Ryza" Stout is painfully ordinary. Despite being the daughter of a hardworking farmer, she would rather go on pretend adventures as she explores almost every corner of the island. However, the fact that it is against the local customs to venture off Kurken Island irritates her to no end. One day, wishing for something interesting to finally happen in her life, Ryza escapes on a boat with her two good friends: the bookworm Tao Mongarten and the aspiring warrior Lent Marslink. Arriving at a nearby forest, the trio stumbles into Klaudia Valentz, the daughter of a visiting merchant who also wandered off into the woods. As the naive and underprepared group ventures further, they run into dangerous monsters. Thankfully, they are rescued by the alchemist Empel Vollmer and his skilled bodyguard Lila Decyrus. This fateful encounter will lead Ryza to the key that will change her life forever—the creative and wonderful world of alchemy.

In Japan, betting on horse racing is one of the few legal forms of gambling; thus, the public races have become an interesting part of Japanese culture. In this sport, an individual who rides a horse and competes in races is called a jockey—that is just what Yuu Arimura aspires to be. Becoming inspired after witnessing a derby, 15-year-old idol Yuu shocks the entire nation when he leaves the entertainment industry to enroll in a prestigious horse racing school. Excited to pursue his latest passion, he gradually bonds with his new classmates—such as the talented Shun Kazanami and the self-assured Amane Grace—who are each unique in their own way. Although the path ahead may be full of obstacles, Yuu is determined to pursue his ultimate goal of becoming one with his horse.

While the young Angelique lives out her days peacefully in her school, attacks from the monstrous Thanatos has been increasing everywhere else. Two Purifiers show up one day, men with the power to exterminate the Thanatos. One of them, Nyx, attempts to convince Angelique to join them in their work, as she has the power to be the only female Purifier. As Angelique hesitates, a Thanatos shows up in their school. Nyx and the other Purifier, Rayne, fight a losing battle. With her classmates falling prey to the Thanatos, and the Purifiers beaten to submission, Angelique's desire to save everyone awakens. She became the only female Purifier in their land of Arcadia, the one known as the "Queen's Egg".

Born from the strong emotions of their creators, self-contained pocket dimensions known as Phenomenon have begun forming across Japan. These false worlds overwrite the reality of an affected area and will only be undone if the maker is defeated or appeased. In response, a military-sponsored task force known as Trinary is formed, and its three members—Miyabi Koigasaki, Gabriela Lotaryńska, and Ayami Kunimasa—specialize in dispersing Phenomenon. Caught in one of these Phenomenon during her favorite idol's concert, Tsubame Ouse is saved by the timely arrival of Trinary, and together they are able to resolve the incident. After these events, Tsubame, along with newcomer Kagura Uzuki, decides to join the current Trinary team. As the girls struggle to balance their everyday lives and their responsibility to handle each new Phenomenon that appears, they realize that their own reality also has its own distinct set of problems.