It was roughly eighteen years after the events of Panzer Dragoon Zwei that the Sestren AI relocated the Heresy Program, the renegade entity that had been ejected from the Ancient Age data network. The Sestren AI once again responded by activating one of the world’s ancient Towers, with the intention of annihilating the Heresy Program once and for all.

This particular Tower protruded from the ocean off the coast of the Empire’s capital city, and it had recently been discovered by the Empire itself. The Tower’s guardian - known as the Dark Dragon - was also awakened, although its place of slumber was far away; the terrible creature had a long journey ahead of it.