The story begins when Dart is heading home from a five-year-long journey to pursue the Black Monster who killed his parents and destroyed his birth city: Neet. On the way, he is attacked by Feyrbrand, a dragon controlled by the Sandora, a rebel faction in the Serdian civil war. After Dart gets hit by the dragon, he gets saved by a mysterious female heroine named Rose, though they soon part ways. When he arrives at his hometown, Seles, he discovers that it has been destroyed by Sandora, and that Shana, Dart's childhood friend, has been taken away. Dart sets out to rescue her. Throughout the game, he is periodically joined by people that he helps along the way.
After rescuing Shana from Hellena prison with the help of Lavitz, a recently escaped knight of Basil, the trio make their escape to the prairie. Continuing their journey to reach Basil, the trio pass through a cave and encounter a snake-like monster known as Urobolus. The monster is defeated by Shana from a mysterious hidden power, leaving the trio confused and the mystery around Shana's powers to begin. When the trio reaches Basil, they go and meet the king to explain the incident at Hellena. King Albert sends the party to defend the fort-city of Hoax against attacks from Sandora. Among the attacking Sandora is Kongol, the last survivor of a race of giants known as the Gigantos. It is in his battle with Kongol that Dart first gains his ability to transform into a Dragoon using a memento from his father that he found after his death, now revealed as the Dragoon Spirit of the Red-Eyed Dragon with the help of Rose. Kongol is injured, but survives and retreats. With the fort safe, they travel to the city of Lohan. In the city, they meet a man named Lloyd in the Heroes Tournament. He is now a playable character.
Dart and the party finally catch up and defeat Lloyd and Lloyd obtains the Divine Dragoon spirit, however, he is unrecognized as the Divine Dragoon. Emperor Diaz then reveals several things to the party. During the height of the Wingly Empire over eleven thousand years ago, they discovered that the 108th fruit in the Divine Tree would give birth to a creature called the Virage Embryo, also known as the God of Destruction, and was meant to end all other life. Before it could be born, the Winglies used their magical power to separate its body from its soul, making it unable to be born. They then cast the body into the sky, where it became the Moon That Never Sets, and sealed it using several magical Signets, one in each of the ancient Wingly cities, to prevent the soul and body from reuniting. The soul of the God of Destruction was originally placed inside the Crystal Sphere, which was worn by the ancient Wingly ruler Melbu Frahma to increase his power. However, during the Dragon Campaign, when the Dragoons assaulted Kadessa, the flying capital city of the Ancient Winglies, the Crystal Sphere was shattered during the fight between Melbu Frahma and Zieg Feld, leader of the Dragoons.
Ever since, the soul of the God of Destruction has wandered the earth and, every one hundred and eight years, possesses the body of a human child (known as the Moon Child) in an attempt to return to its body. The body can be summoned if the Signets are destroyed, which can be done using the immense magical power contained within the artifacts that Lloyd gathered.
Emperor Diaz then reveals himself to be Zieg, Dart's father and leader of the Dragoons that fought in the Dragon Campaign. After Zieg defeated Melbu Frahma, Melbu cast a spell that both petrified Zieg and kept Melbu's spirit alive within Zieg's dragoon spirit. Thousands of years later the petrification wore off, and Zieg settled down to start a family in Neet. Finally, it is revealed that Rose was both Zieg's lover and fellow Dragoon during the Dragon Campaign, and was granted immortality by the remaining Winglies in order to kill the Moon Child every 108 years, and has since become known as the Black Monster. Rose destroyed Neet in an effort to locate and kill the Moon Child, although Zieg reveals that the child Rose killed was the twin sister of Shana, the actual Moon Child, whom he then kidnaps. Zieg leaves to destroy the Signets.
Zieg flees and proceeds to destroy the remaining three Signet Spheres that seal the Moon That Never Sets, causing it to fall from the sky and land on the Divine Tree. He then carries Shana to the body of the God of Destruction, so that the body will sense the presence of its soul and prepare to restore itself. The party arrives to stop Zieg, who steals the Red Dragoon Spirit back from Dart and fights the party. After his defeat, it is revealed that years ago, Zieg attempted to use his Dragoon Spirit to fight the Black Monster attacking Neet, but Melbu Frahma emerged and possessed him. Frahma unites with the body himself, taking the form and power of the God of Destruction. Zieg is released from Frahma’s possession.
In his final moments, Lloyd gives the Divine Dragoon spirit to Dart and the Dragon Buster to Rose. The party defeats Melbu Frahma, but at the cost of Rose and Zieg, who sacrifice themselves to destroy the God of Destruction. Everybody else is able to return home.
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