Far from the city's noise lies Torishirojima—a quaint and peaceful island where time seems to move slowly. Hairi Takahara, a young boy nursing a wounded heart, uses the recent death of his grandmother as a quiet reason to leave the city for a summer retreat to Torishirojima. Upon reaching the island, Hairi finds himself surrounded by a refreshing, laid-back atmosphere, a far cry from the hustle and bustle he is used to. After moving in with his aunt, Kyouko Misaki, he prepares to spend the summer helping her sort through a shed full of artifacts his grandmother collected over the years alongside his cousin, Umi Katou, who is staying with them. While adjusting to the island's slower pace, Hairi decides to spend his free time exploring. He soon meets the cheerful Tsumugi Wenders; the antisocial Shiroha Naruse; the wandering Kamome Kushima; and the sharp-tongued Ao Sorakado. Drawn into their lives and the island's subtle mysteries, Hairi is gradually swept up in a summer filled with fun, nostalgia, and life-changing moments that will stay with him forever.

Centuries ago, Kanna, a princess and the last of a winged race, was held prisoner in a castle as she was feared by the rest of the world. However, when she met a soldier named Ryuuya, she fell in love with him and told him of her wishes to see the outside world and to find her mother. Ryuuya attempted to fulfill these wishes. However, his efforts were in vain as Kanna was sealed in the sky through magic and cursed to be in pain for all eternity. Hundreds of years later, Yukito, a decendant of Ryuuya, comes to a quiet town one week before their annual festival with hopes that he can make some money. However, when he meets an unusual girl called Misuzu, he is reminded of what his mother once told him—When you go out on your journey, if you find the winged girl's re-incarnation, you must use your power to set her free. Yukito and Misuzu's fates soon become intertwined with each other, with each developing feelings for the other. However when Yukito realizes Misuzu's connection to the past, he must decide on whether to leave, or to attempt to break the curse that has bound Kanna in centuries of pain.

Death is one of many mysteries that has left humanity in the dark since the dawn of time. However, the burning question of what happens to the soul after one dies is soon answered to 17-year-old Yuzuru Otonashi. Waking up with no previous memories in a dimension between life and death, he discovers the unsettling truth of the afterlife. Taking the form of a high school, this bizarre dimension is designated to shelter those who died unwanted deaths. Feeling wronged by God during their earthly lives, the school's residents have decided to form the Afterlife Battlefront—a rebellious faction determined to oppose their god-like student council president, Kanade Angel Tachibana. The group's leader, Yuri Nakamura, recruits Otonashi in their fight against Angel in order to take control of their own lives. However, questioning the morality behind their actions, Otonashi takes a step behind the enemy lines to understand the opposing side of their common fate.

If not for his ability to take over people's mind and body, Yuu Otosaka would be an ordinary high school student. Though it only lasts for five seconds at a time, Yuu's mysterious power allowed him to cheat his way to the top of his class and enter a prestigious high school, where he continues his dishonest acts. His shenanigans are eventually stopped by Nao Tomori—the headstrong student council president from Hoshinoumi Academy—who sees through his deceit. Through coercion, Nao convinces Yuu to transfer to Hoshinoumi and join the student council. Hoshinoumi Academy is secretly an institution created for adolescents who possess supernatural abilities—with the student council serving as a means of locating those who abuse their powers. With Yuu begrudgingly assisting in council affairs, the group sets out to find and protect new ability users from harm. However, as they further investigate the abilities, their findings entangle them in far more complicated matters than they could ever imagine.