On a remote island far from the mainland named Urashima, a man washes ashore, with no recollection of his name or homeland. What he does recall, however, is that he is a time traveler with a mission: to save a certain girl from harm. As nightfall arrives, he meets Rinne Ohara, a girl who sings a tune that reminds him of a specific name—Setsuna—and decides to use it as his own. Knowing another Setsuna herself, Rinne takes him to her household as a servant, hoping that he is the same one she remembers. On the other hand, Setsuna continues to learn more about Urashima, desiring to identify his lost past. He comes to know about the island's folklore, its three great families, and the endemic disease that prevents anyone afflicted from stepping out into the daylight. As the mysteries of his missing memories and Urashima itself unfold, Setsuna must remember his purpose and fulfill his mission as soon as possible. But, as he witnesses the myriad of troubles plaguing the island, Setsuna begins to question—is his temporal displacement merely an effort to change a single girl's fate?

Teenager Yamato Akitsuki has moved from the Hiroshima countryside to Tokyo to begin his high school career. In return for room and board, he has agreed to help his aunt and cousin run their bathhouse and the adjacent girls-only dormitory where he will be staying. On his way to meet his relatives, he passes by a local high school track and is mesmerized by a high jumper practicing her technique. Later on, Yamato finds out that the high jumper is not just another resident of the dorm, but is also his neighbor. Suzuka Asahina is a heavily scouted track and field athlete who is attending the same high school he is enrolled in. A perfectionist by nature, Suzuka is put off by Yamato's clumsy and carefree attitude and finds it difficult to be near him. Determined to win her over, Yamato joins the track team after discovering his hidden talent for sprinting. Through his interactions with the track team, his classmates, and the ever-inebriated college students in the dorm, Yamato finds the resolve to become a better athlete and a more suitable companion to Suzuka, even if it means pushing himself to the point of exhaustion.

Long ago, there was a monk named Myoue who could bring anything he drew to life. He quietly lived with his wife Koto—a black rabbit in human form—and their three children: Yakushimaru, Kurama, and Yase. One day, the high priest of the land concluded that Myoue's drawings caused too many problems for the locals and ordered him to find a solution. In response, the family secretly fled to an alternate world of Myoue's own creation—the Looking Glass City. Everything was peaceful until Myoue and Koto suddenly vanished. Their three children are left to take care of the city, and Yakushimaru inherits Myoue's name and duties. Stranded in this alternate world, their problems only get worse when a young girl—also named Koto—crashes down from the sky and declares that she is also looking for the older Myoue and Koto. Armed with a giant hammer and two rowdy familiars, Koto just might be the key to releasing everyone from the eternal paper city.

While taking a ferry to Fuuka Academy, new students Mai Tokiha and her sickly younger brother, Takumi, spot a girl adrift on the water. Shortly after bringing her aboard, the ferry comes under attack from an assailant who summons a mechanical monster. Despite still recovering from her injuries, Mikoto Minagi fends off the monster using a supernatural sword. Mai soon discovers that Mikoto is a fellow Fuuka Academy student with abilities called HiME (Highly-advanced Materializing Equipment). Female students with HiME are responsible for defending the academy and the local city from the monstrous Orphans. After several incidents at the school involving battles against these mysterious creatures, Mai learns that she is a HiME herself and is capable of summoning a Child, a mechanical creature capable of great utility and firepower. Now burdened with new responsibilities, Mai joins 12 other HiME as they safeguard the school from a threat they know little about all while protecting the ones closest to them.