This way it works off as a prequel — he created Myria, sent the world into a Medieval Stasis, and this lead to Breath of Fire I.
After Ryu casts out the Gods at the end of the game, he remains behind as a mortal. However, some latent dragon powers remained and grew after several generations, giving birth to the Dragon clan, a.k.a. the Brood. Meanwhile, Yuna created his own artificial Endless, the goddess Myria (he may also have given Deis a body of her own). The Dragon clan fought the Goddess, leading to the events of BoF I, then II, and finally III. After Myria's defeat in III, the Desert of Death covered the world, forcing the people underground as seen in Dragon Quarter.