In the 11th year of the Meiji Era, the end of the samurai shogunate and the prohibition of swords has left Japan with lasting scars. Displeased by these recent changes, many former samurai plot against the new government, inciting a wave of bloodshed. To counter this movement, the government constructs a colossal prison in the middle of Lake Biwa. Unofficially assigned to help the police arrest criminals, Tenka Kumou also serves as a ferryman to the Lake Biwa prison with the help of his two younger siblings: the ambitious Soramaru and the enthusiastic Chuutarou. Together with the former Fuma ninja Shirasu Kinjou, the Kumou brothers live a frugal and joyful life mostly dedicated to studying and training. However, behind this relatively uneventful daily routine, the specter of the Orochi curse is starting to spread its shadow over the city of Oumi. According to legend, every three hundred years, Orochi reincarnates in a human vessel—and it is believed that this is the harbinger of an imminent catastrophe. As various groups clash in search of Orochi's vessel, some aim to seal the curse, while others have darker plans in motion.

After succumbing to an unenviable fate, Kiritsugu Emiya has left Shirou Emiya the duty to save mankind in his place. The world is dying and time is ticking, but when the salvation Shirou seeks is at the cost of his only family left—his younger sister—will he still have the heart to pursue this duty? Shirou is now pressed with the choice to continue being a hero of justice—or become the very evil his ideal has vowed to vanquish. The orphan is alone once again, yet his body is still made of swords. The Fifth Holy Grail War now begins with his oath under snow.

Rika Furude and Satoko Houjou are best friends who have lived in the small village of Hinamizawa for their entire lives. Alongside their other friends, they spend every day together, and every moment is filled with fun and laughter. However, as Rika and Satoko begin to grow older, a life-changing opportunity presents itself to both of them. Rika is determined to follow her dreams and wants Satoko by her side. Although Satoko is hesitant, she decides to walk this path with Rika. However, the realization of her dream forms a rift between them. This leaves the girls living in completely different worlds, with Rika enjoying her new life and making new friends while Satoko grows more and more isolated. Longing to return to the nostalgic days in Hinamizawa, Satoko despairs and wishes things could be changed. Just when she is at wits' end, an encounter with a supernatural entity changes Satoko's perception and imparts new revelations about her best friend Rika. This begins her journey to get the future she desires—by any means necessary.

Logic is the concept that governs emotions, abilities, ideals, memories, and all other abstract properties that make up life in various worlds. With its power, however, alien Foreigners are able to pass through portals imbued with their respective world's Logic and pose a threat to other worlds. To counter this problem, the Another Logic Counter Agency (ALCA) from the human world of Septpia employs Logicalists, people with the power to form bonds with the Foreigners who seek peace and share their Logic, tasked with dealing with all possible dangers. After overloading his powers two years prior, Yoshichika Tsurugi has lost the ability to use Logic in combat, making him no different from a regular citizen. However, his life soon returns to the battlefield when he meets Athena, a Foreigner goddess from the world of Tetra-Heaven. She brings Yoshichika his missing Logic Card, allowing him to become a Logicalist once again. Soon after, Yoshichika forms a contract with Athena and joins ALCA. There, he meets other Logicalists, and only by working with them can he hope to bring an end to the threats once and for all.