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The confrontation between the Earth Alliance (Naturals) and Zaft (Coordinators) originated in economic trouble had reached an impasse. War couldn't be stopped by that point, and thus this story begins one year later when Heliopolis, a resource satellite belonging to a neutral nation, is suddenly attacked by a Zaft mobile suit force.

The game and anime follow Kon Hokaze, a boy who embarks on a journey from our world to an alternate world known as Mira, which is full a mysterious energy known as Alma. After saving Princess Ecarlate from attackers, he soon finds himself in the middle of a struggle around Alma.