Blood of Bahamut is set in a world in which people have built their cities on the backs of sleeping giant beasts. Suddenly, the beasts wake up and people find that their home towns are now their enemies.

In the main story, you take control of Ibuki, a young man who resides in a town on the back of the giant beast Giganto. Ibuki is considered to be of the "Giganto" race. He will fight alongside Yui, a childhood friend who witnesses the awakening of the beasts and fights to protect her home town.