The overall plot is very similar to the first story arc in the manga and anime, with eight-grade girls Hikaru Shidou, Umi Ryuuzaki and Fuu Hououji finding themselves drawn from their respective field trips to the Tokyo Tower into the world of Cephiro.
Unlike in the manga and anime, all of Zagato's minions die throughout the game, including Ascot, Caldina and Lafarga (named as Rafarga in the English version).