After discovering a mysterious sword in the storehouse of her home, third-year high school student Yui Kusanagi finds herself suddenly transported to a different world. While exploring her new surroundings, she meets five strange yet handsome men before coming face to face with Zeus: the king of the gods. In order to restore the deteriorating relationship between the gods and humans, Zeus has created the Academy of the gods and has chosen Yui to be its one and only instructor. She has one year to educate the young and reluctant deities—including the five strangers she met earlier—on what it means to be human while learning about the gods herself; otherwise, they will all be trapped in Zeus' realm forever.

Nanami Momozono and her familiars Tomoe and Mizuki have survived quite a few challenges since Nanami took up the mantle of Mikage Shrine's patron god. Naturally, the wind god Otohiko comes to invite Nanami to the Divine Assembly in Izumo, the home of the gods, and Nanami chooses to take Mizuki with her, leaving Tomoe to pose as her at school. However, she has an ulterior motive for attending the Divine Assembly: to discover the whereabouts of the missing Lord Mikage, the former god of the shrine. After her adventures in Izumo, Nanami meets Botanmaru, a tengu child looking for someone she knows all too well—tengu turned goth idol Shinjirou Kurama. Botanmaru needs Shinjirou, their prince, to return home to Mount Kurama and stop the tyranny of Jirou, who has taken over the rule of their hometown. However, Nanami soon discovers a force much darker than Jirou is at work on the mountain. As a fledgling god becoming more accustomed to divinity, Nanami finds herself dealing with a tengu rebellion, her blooming feelings for Tomoe, and a strange man with ties to both Tomoe's past and Nanami's future.

Sixth-grade student Kanna Hayama's love of running becomes a source of grief when she loses her mother Yayoi, whom she shared this passion with. However, her disposition changes after she accidentally discovers an astonishing truth about Yayoi. One day, Kanna unexpectedly encounters a divine messenger in the form of her favorite rabbit Shiro and a demon boy named Yasha. They reveal to the girl that her mother was an Idaten—a descendant of the gods endowed with incredible speed and entrusted to bring offerings from all over Japan to the annual Kamiari Festival in Izumo. As Yayoi's daughter and the new possessor of the Idaten amulet, Kanna is expected to take over this responsibility; otherwise, there will be dire consequences for the country's fate in the year to come. Enticed by the prospect of seeing her mother once more at the deities' event, Kanna accepts the challenge and enlists Shiro and Yasha to help her on her quest. Unbeknownst to her, there is more than meets the eye to this marathon-like journey that will test not only her physical condition but also her heart's resolve.

While playing in the snow one day at her shrine, the land god Nanami Momozono witnesses her familiar—the fox youkai Tomoe—collapse, with dark markings appearing on his body. Tomoe's former master, Lord Mikage, appears after his long absence and places Tomoe into a magical pocket mirror in order to stave off his ailment. Mikage explains that long ago, before he and Tomoe had met, the fox youkai was in love with a human woman. Seeking to live as a human with his beloved, he made a deal with a fallen god, but he only ended up cursed and dying. When Mikage discovered Tomoe, the god made the youkai forget his human love as a quick solution. However, something has changed recently to reactivate the curse; Tomoe has fallen in love with his new human master, Nanami. Since there is no way to stop the curse, Nanami wants to stop Tomoe from getting cursed in the first place by traveling back through time, even if it means they may never meet. As Nanami travels back hundreds of years to save her precious familiar, she discovers that she is far more closely bonded to Tomoe than she previously thought.