Thousands of years before the events of Skies of Arcadia, six civilizations coexisted on floating continents in the titular skies of Arcadia, a world with no apparent surface that is orbited by six moons of different colors. 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, as well as the Moon Crystals that could be used to control them. Using the Gigas, the civilizations warred with one another, which caused enormous environmental harm and threatened the extinction of all six civilizations. The most advanced of the civilizations, 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 destroying the other five civilizations, thus ending the war. A seal was placed on the Silver Gigas to prevent the Rains from being used again, and the Moon Crystals were hidden away.
In present time, the militant and tyrannical Valuan Empire, led by Empress Teodora, seeks the Moon Crystals in order to awaken the Gigas and take over the world. Valua's will is enforced through the Valuan Armada, a fleet of iron-clad warships led by senior admiral Galcian and vice admiral Ramirez under the authority of the Empress. They are primarily opposed by the Blue Rogues, a faction of Air Pirates who make it a point to harass the Armada as much as possible. Fina, a young girl from the Silver Civilization, is sent to find the Moon Crystals before the Valuans and bring them to a safe place.