Yggdra Unison begins in the year 1490 M.D., with Emperor Gulcasa—the ruler of the New Bronquian Empire—and his vast army attacking and capturing Fort Karona, which lies on the border between his own nation and that of the Kingdom of Fantasinia, the country perceived to be the greatest world power. Fantasinia's defeat and the death of its king shock the world, but unlike the events of Yggdra Union, this shock causes every major world power to strike out in an attempt to conquer the continental world. The player selects one of these nations, and their storyline unfolds as they conquer other territories, eventually culminating in their achieving world domination. Because of the sandbox-style gameplay, the game focuses more on character interaction and gameplay itself than a linear plot; there are twelve storylines, each following one of the twelve playable characters.