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.

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.

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.