In Eternal Aselia, you command a group of young female characters called "Spirits" in strategy battles while working to build a kingdom and build a relationship with a girl. The story centers on main character Yuuto Takamine, a student who resides with his younger sister, Kaori. Yuuto and his sister lost their parents in their childhood and were brought into the care of another family. That family was lost in an airplane accident which Kaori, miraculously, survived. One day, Yuuto encounters a mysterious girl called Tokimi Kurahashi, and his mind goes blank. In his limited consciousness, he hears Tokimi tell him, "The time has come for you to pay the price... the price of the miracle."