Star Driver takes place on the fictional Southern Cross Isle. One night, a boy named Takuto washes up on shore swimming from the mainland. He later enrolls in Southern Cross High School as a freshman and makes new friends.

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 story takes place in the wintry land of Shantia, with Manatsu and the others invited to the land by its princess Sharon. But as they arrive, a mysterious monster attacks Shantia, and it is closed off to outsiders.

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.