On the day of Valen's initiation, a ceremony where candidates receive blessings from each of the six dragons, the Black Dragon attacks. The Water Dragon attempts to thwart the attack, but is critically injured. During the attack, Valen comes to the aide of a girl, Euphe, who becomes smitten with her hero.
Valen and a group of Dragoons set out to discover the fates of the six dragons, receive their blessings and defeat the Black Dragon. As a show of trust, Valen is given the fire orb while Euphe mysteriously comes into possession of the water orb.
Dragoneer's Aria is a different look from what Nippon Ichi usually publishes. Rather than using a 2D anime-inspired look, the game employs 3D characters and environments that exhibit a much different art style. The overall story has a more serious tone that matches the darker color palette.