Guardian's Crusade takes place in a fantasy world where a battle between good and evil unfolds. The player takes on the role of Mickey (or another name chosen by the player), a young boy who stumbles upon a Guardian, a "protector" resembling a monster. Upon meeting the Guardian, who has been awakened from a long slumber, the Guardian explains that he was created to protect the world from an impending evil. However, the Guardian has lost his memory of being a protector with an important mission. The world is now facing growing darkness due to the return of a powerful enemy that aims to destroy it. Together, Mickey and the Guardian embark on a journey to restore the Guardian's power and memories and to stop the looming threat.