Yorito Morimiya is obsessed with the sky. He especially loves taking pictures of its array of different faces—sunrises, sunsets, clouds. On one of his early-morning excursions to photograph the sunrise, Yorito meets a strange girl engaged in an argument with a vending machine. By the time that Yorito forces the girl's tomato juice out of the machine, she's vanished without a trace. Sola follows the story of Yorito, his sister Aono, and their childhood friends Mana and Koyori Ishizuki, as well as that of a mysterious girl who appears and disappears, and who seems to harbor a dark secret. In a world where magic and the supernatural are never far below the surface and no one is who they seem to be, love and loneliness vie for supremacy beneath Yorito's sky.

The all-girls Kikyo Private Academy and Chidori Public High School are polar opposites. With its prestigious history, Kikyo is attended by noble young ladies from distinguished families, while Chidori is infamously full of simple-minded delinquents. It is no surprise that their students clash with their differences. Having a tall stature and fierce appearance, Chidori student Rintarou Tsumugi is often avoided by others despite his gentle heart. One day, while helping out at his family's patisserie, he meets a customer who, after a brief moment, runs away from him. The next day, the customer returns to apologize to Rintarou, introducing herself as the cheerful Kaoruko Waguri. After spending time with Kaoruko, Rintarou appreciates that she does not judge him based on his appearance and looks forward to when they will meet again. However, when Rintarou discovers Kaoruko attends Kikyo, their relationship will challenge the social expectations and dynamics around them.

Two years after the battle against Eosmon, Davis Motomiya, Ken Ichijouji, Yolei Inoue, Cody Hida, T.K. Takaishi, and Kari Kamiya meet a boy named Rui Owada, who is found with a depowered Digivice and claims to be the first Digidestined ever. In addition, a Digimon named Ukkomon appears in the real world, who wants every person in the world to have their own Digimon partner.

8-year-old Hiyori, who lost her parents, and Yui, seeking to escape her violent father, got off at a Kitsunezaki station one day. The great earthquake and tsunami had changed their destinies. Their lives were saved, but they were perplexed when asked about their identities at an evacuation site. It was an old woman named Kiwa Yamana who lent them a helping hand. From that day, Yurie was known as Yui, Moeka as Hiyori, and together with Kiwa, the three women began a wonderful communal life together at the old house "Mayoiga" overlooking the sea.