The game starts off with the player as the main protagonist, called Tatsuya as the default name, and introduces us to his best friend, whose default name is Miki. The story kicks off with Tatsuya and Miki sitting on a bench. Tatsuya is too immersed in the game he is playing on his PSP to notice that Miki is missing. Kratos, Miki's dog, barks and shows Tatsuya where Miki is and thus he finds her unconscious on the ground, sick by some unknown illness. He wishes for her to become better, and suddenly, a voice magically appears and asks Tatsuya if he wants to save his friend and make her healthy again. He agrees and thus the adventure begins in an unknown land separated from the rest of the world in order to seize 5 different gems for the Traveler's Sword he holds so he can return to his own world and restore Miki back to good health.

The game is based on the Japanese novel Brave Story by Miyuki Miyabe, and features some of the original cast, although the main characters Tatsuya and Miki (as well as most of Tatsuya's party) are original creations for the game.