A technological hell masquerading as paradise, Tsukimihara Academy is an artificial high school that serves as the setting for the next Holy Grail War. Created by the Moon Cell computer, the school is inhabited by Earth-projected souls who have even the slightest aptitude for being a "Master." Of these 256 souls, 128 will be chosen for the main tournament and granted a Servant. With all of the Masters selected, the Academy activates a purge, targeting the remaining lifeforms for elimination. Awakening in a pool of his own blood, Hakuno Kishinami refuses to die. Fueled by unknown feelings of hatred, he vows to fight for survival. As he struggles to escape from a relentless pursuer, he finds a crimson blade plunged into the ground; and by pulling it out, Hakuno summons his own Servant, Saber, who instantly destroys his pursuer in a flurry of rose petals. With his newfound power, Hakuno must now begin his journey to Moon Cell's core, the Angelica Cage. There, he will unveil the reason for this artificial world and the secrets of his own blood-soaked past. [Written by MAL Rewrite]

Deep in a tropical jungle, young Yaiba Kurogane diligently practices swordsmanship alongside his father, Kenjuurou, completely unaware of the modern world. However, one day, the two end up in a container on its way to Japan. There, they encounter Kenjuurou's old rival, Raizou Mine, and his daughter, Sayaka. Out of other options, Yaiba agrees to a deal with the Mine household: if he beats the strongest student in their dojo, he will be welcome to stay. Using his distinctive skills and extraordinary strength, Yaiba earns his place. Wanting to fight more powerful enemies, Yaiba follows Sayaka to school—where he quickly loses to Takeshi Onimaru and acknowledges him as his new rival. With Onimaru inheriting the sword of his bloodline and obtaining demonic powers, Yaiba must train to become even stronger and beat him for good.

After surviving the entrance exams, Sakuta Azusagawa has finally enrolled in the same university as his girlfriend, Mai Sakurajima. He is gradually getting used to the unfamiliar environment as he attends student gatherings and makes new acquaintances. Everything seems to be going smoothly until Sakuta's friend and Sweet Bullet idol group member Uzuki Hirokawa begins acting out. With fellow Sweet Bullet member Nodoka Toyohama pleading for his help, Sakuta realizes that he has stumbled upon another case of the inexplicable Puberty Syndrome—Uzuki is feeling pressured by the sudden surge of popularity and rumors of a potential solo career. While Sakuta searches for a solution, another occurrence of Puberty Syndrome gradually emerges from the shadows.

The all-girls Kikyo Private Academy and Chidori Public High School are polar opposites. With its prestigious history, Kikyo is attended by noble young ladies from distinguished families, while Chidori is infamously full of simple-minded delinquents. It is no surprise that their students clash with their differences. Having a tall stature and fierce appearance, Chidori student Rintarou Tsumugi is often avoided by others despite his gentle heart. One day, while helping out at his family's patisserie, he meets a customer who, after a brief moment, runs away from him. The next day, the customer returns to apologize to Rintarou, introducing herself as the cheerful Kaoruko Waguri. After spending time with Kaoruko, Rintarou appreciates that she does not judge him based on his appearance and looks forward to when they will meet again. However, when Rintarou discovers Kaoruko attends Kikyo, their relationship will challenge the social expectations and dynamics around them.