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.

Deep in the forest, far from any human contact, there lives a child named Ryouma Takebayashi. He engages in the rather strange hobby of keeping various types of slimes as pets. Furthermore, despite his young age, he has a sturdy physique and good compatibility for magic. All of this is because, having endured much hardship in his previous life, three gods grace Ryouma with a second chance to pursue one goal: savor the wonders of life. After three years of comfortable solitude pass by, Ryouma meets people that will change his current life forever. When he encounters and helps some soldiers tend to their wounded comrade, the group convinces him to accompany them to visit the nearby town's ducal family. Ryouma agrees and soon embarks on a journey to explore the vast world beyond his home.