Arcadia is a world where continents float high above, and people travel by airships. Among the countries of this world, the most powerful one is the Empire of Valua. Guided by its greedy admirals, Valua strives to possess all the power in Arcadia. The boy Vyse and the girl Aika are members of the Blue Rogues - noble pirates who attack only Valuan war ships. During one of their confrontations with a battle ship, they encounter a girl named Fina, who is on an important mission whose secret she cannot tell yet. Involved in the conflict with the Empire of Valua, the trio of the heroes must explore the whole world of Arcadia in order to defeat the admirals.

The game takes place in the fictional skies referred to as Arcadia, where six civilizations coexist on floating continents orbited by six moons of different colors. Thousands of years prior to the present time of the game, the civilizations, one of which existed for each moon, developed technologically to the point where each created a Gigas, a colossal living weapon of mass destruction, controlled by a Moon Crystal. Using the Gigas, the civilizations warred with one another, threatening the extinction of humanity. The most advanced, the Silver Civilization, used their Gigas to summon the Rains of Destruction, which pulled meteors from the orbiting moons and crashed them down onto the planet's surface. The catastrophic destruction stopped the rampage of the Gigas, as well as nearly destroyed the other five civilizations, thus ending the war. A seal was placed on the Silver Gigas to prevent it from being used again, and the Moon Crystals were hidden away, while each civilization worked on rebuilding itself.

Vyse and Aika are members of the Blue Rogues, a faction of Robin Hood-minded air pirates gathered together to resist the militant and tyrannical Valuan Empire. Led by Empress Teodora, the empire seeks the Moon Crystals to reawaken the Gigas and take over the world. Teodara directs the Valuan Armada, a fleet of warships led by admirals Galcian and Ramirez, to find them. Upon the Silver Civilization learning of this plan, they send Fina to find the Moon Crystals first. She is captured by the Armada, but saved by Vyse and Aika, who, with mutual enemies, agree to help her mission.