Cocona is an average middle schooler living with her grandmother. And she who has yet to decide a goal to strive for, soon met a strange girl named Papika who invites her to an organization called Flip Flap. Dragged along by the energetic stranger, Cocona finds herself in the world of Pure Illusion—a bizarre alternate dimension—helping Papika look for crystal shards. Upon completing their mission, Papika and Cocona are sent to yet another world in Pure Illusion. As a dangerous creature besets them, the girls use their crystals to transform into magical girls: Cocona into Pure Blade, and Papika into Pure Barrier. But as they try to defeat the creature before them, three others with powers from a rival organization enter the fray and slay the creature, taking with them a fragment left behind from its body. Afterward, the girls realize that to stand a chance against their rivals and the creatures in Pure Illusion, they must learn to work together and synchronize their feelings in order to transform more effectively.

Ohana Matsumae is an energetic and wild teenager residing in Tokyo with her carefree single mother. Abruptly, her mother decides to run away with her new boyfriend from debt collectors, forcing the young girl to fend for herself—as per her mother's "rely only on yourself" philosophy—in rural Japan, where her cold grandmother runs a small inn. Driven to adapt to the tranquil lifestyle of the countryside, Ohana experiences and deals with the challenges of working as a maid, as well as meeting and making friends with enthralling people at her new school and the inn.

Rika Furude and her group of friends live in the small mountain village of Hinamizawa; in June 1983, they welcome transfer student Keiichi Maebara into their ranks, making him the only boy in their group. After school, they have fun playing games and spending each day living their lives to the fullest. Despite this seemingly normal routine, Keiichi begins noticing strange behavior from his friends, who seem to be hiding the town's dark secrets from him. Elsewhere, a certain person watches these increasingly unsettling events unfold and remembers all the times that this, and other similar stories, have played out. Using that knowledge, this person decides to fix these broken worlds. However, when certain variables change, the individual is faced with a horrifying realization: they have no idea what to expect or how to stop the impending tragedy.

During the summer of her freshman year of high school, Yuzu Aihara's mother remarried, forcing her to transfer to a new school. To a fashionable socialite like Yuzu, this inconvenient event is just another opportunity to make new friends, fall in love, and finally experience a first kiss. Unfortunately, Yuzu's dreams and style do not conform with her new ultrastrict, all-girls school, filled with obedient shut-ins and overachieving grade-skippers. Her gaudy appearance manages to grab the attention of Mei Aihara, the beautiful and imposing student council president, who immediately proceeds to sensually caress Yuzu's body in an effort to confiscate her cellphone. Thoroughly exhausted from her first day, Yuzu arrives home and discovers a shocking truth—Mei is actually her new step-sister! Though Yuzu initially tries to be friendly with her, Mei's cold shoulder routine forces Yuzu to begin teasing her. But before Yuzu can finish her sentence, Mei forces her to the ground and kisses her, with Yuzu desperately trying to break free. Once done, Mei storms out of the room, leaving Yuzu to ponder the true nature of her first kiss, and the secrets behind the tortured expression in the eyes of her new sister.