Nine years ago a mechanical engineer named Sheila Min was sailing back to mainland Japan when a rogue wave threw her overboard. Nearly drowned, she inexplicably washes up on the shores of the mythical Himitsu Island, where she rescues a dying infant dragon. Fearing for the young dragon's life, Sheila decides to live on the mysterious island and names the baby dragon Onyx.

As Sheila and a nine-year-old Onyx set off to explore the island and search for gemstones to complete a powerful new arm cannon, they soon find themselves caught in the middle of an approaching war. A group of creatures led by the vile Magus have gained dominion over the islands peaceful inhabitants, and the small factions that remain must rise up and protect the precious little freedom they have left.