The game begins with a girl named Kukuru who is a member of the Sacred Clan in Seirya, a clan that protects the Flame Cion. She is sent by the mayor of her town to extinguish this flame, but once she does, a monster called an Ark Ghoul appears and Kukuru flees. Meanwhile, a boy named Arc prepares to look for his father Yoshua, who has been missing for ten years. He stumbles upon Kukuru and they both defeat the pursuing monsters. Arc makes a promise to Kukuru to reignite the flame for her, but he is quickly struck down by the powerful Ark Ghoul. As he lays defeated, Arc hears a voice call out to him. The voice is a Guardian, who revives Arc and tells him to reignite the flame. The Guardian also tells Arc that he will return here later to extinguish the flame and retrieve the Ark, a mystical box which will aid him in protecting the world; the Guardian finally adds that Arc's father made an agreement with the Guardians of the planet to protect humanity by the forecoming darkness. After hearing this, Arc reignites the fire and resealing the Ark Ghoul before it could kill Kukuru.

Days later, after hearing of Arc's abilities, the king of Seirya summons him to Palencia Castle. As Arc heads to Palencia, Kukuru decides that it is her destiny to help him. Arc explains to the king that the guardian at the mountain had granted him power. In order to see if Arc truly is blessed by the guardians, the king's minister, Andel, insisted that they test him. The two were sent to battle some monsters where the party meets Poco of the drum corps, who was the only survivor from their latest patrol. After Arc returns, the king tells him that he must seek out the Ark in order to save humankind. The king recounts how his own brother, the former king, believed this story and has disappeared to find the Ark. He then tells Arc to seek an audience with the Forest Spirit of Toyoke Forest in Millmana.