The story begins when a group of islands called Kark Isles appear near Ryza's—the protagonist's—hometown. Seeing this as a threat to their home, Ryza and her friends investigate the isles and discover ruins with a huge gate. Just as Ryza approaches the gate, a strange voice echoes in her head, telling her to reach the Code of the Universe. What is it that lies beyond the gate, and what does the "Code of the Universe" mean? In hopes of finding a way to save their home, Ryza and her friends set off on a great adventure that revolves around a Key and the roots of alchemy.