Nanami Momozono, current land god of Mikage Shrine, and her fox familiar Tomoe have faced many obstacles during their time together, but none so challenging as the one posed by the wealth god Ookuninushi—if Tomoe's wish to be human is granted, he must learn to live as one, and Nanami will have to return to being a human. As the couple look to the future and reflect on their former adventures, Nanami tries to figure out their new living situation as her high school graduation approaches. But no matter the path they choose to walk, Tomoe and Nanami's love will endure.

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.

Sora Naegino has finally consolidated herself as Kaleido Stage's greatest star ever, and a new star starts to shine as Rosetta Passel is selected to participate in the next attraction in a main role. But when things start to go wrong in the rehearsals, Rosetta starts to question her abillity to take the role, as her own capacity to remain in Kaleido Stage. Meanwhile, Fool also struggles with his demons from the past.