The game follows the adventures of Ryu (the protagonist) who is the sole survivor of the Dragon Clan, as he struggles to discover why his clan was wiped out. The adventure takes him to many places, on journeys thought impossible, and in the end he will discover power in the ability to choose his own future.

As the last survivor of the Dragon Clan, Ryu must continue his struggle against the evil goddess Myria, who has taken over the world and now controls it.

To fill in the timeline, this occurs after Breath of Fire II. In a large fresco in a secret Brood (Dragon Clan) stronghold, portrays the Breath of Fire I characters battle with a woman with snake like tentacles (Tyr/Myria). The battle with Deathevan is not mentioned, so it can be assumed that Deathevan never reappeared or is never going to become a recurring villain.

The Third episode of Breath of Fire is also the first made for the playstation. As in other episodes of the series, you control Ryu, member of the dragon clans. At first, you're trapped in a giant ice crystal, but miners soon set you free. This is the start of a long journey where you'll search your origins. In fights (turn-based, as in most console RPGs), you have the ability to turn into a dragon. Will that be enough to get out of all the troubles awaiting?