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After saving Luxendarc with the aid of her allies, Agnes Oblige became the spiritual leader of the Crystal Orthodoxy. She immediately set about persuading the Crystal Orthodoxy and the Duchy of Eternia to form a peace and, following years of animosity and endless effort on Agnes' part, a truce between the two is finally near. Flanked by her bodyguard Yew Geneolgia, a bright young soldier of the Crystalguard, Agnes hosts a ceremony to declare a peace between the two parties. But just as the peace treaty is about to be signed, a mysterious man known only as Kaiser Oblivion and his forces invade the ceremony, attacking Agnes and critically injuring Yew in the process.
Yew later awakens from a coma, only to discover that Agnes has been abducted and the Crystalguard has been left devastated. Determined to rescue Agnes, Yew goes in pursuit of Kaiser Oblivion's flying fortress, the Skyhold. As he embarks on this grand adventure, Yew meets supporters, including Edea Lee, now head of the Eternian Ducal Guard, and an enigmatic girl from the moon called Magnolia Arch. Together, these allies must save Agnes and restore the peace once again.