Edge is one of the soldiers in the service of the mighty Empire. The Empire has recently ordered some excavations at ancient ruins, trying to discover the secret of an old technology that is much superior to that of present time. During the excavation works, Edge encounters a mysterious young girl. He then witnesses the murder of his captain and other soldiers by Crayden, one of the Empire's officers. Coming into contact with an ancient dragon, Edge begins to roam the world, determined to find Crayden and avenge the death of his comrades. Nobody helps him but his faithful dragon. But the Empire is also after Crayden, so there appear to be at least three sides in the conflict - or are there more?

Panzer Dragoon Saga is set in the same universe as the other Panzer Dragoon games, but differs from the rest of the series by being a role-playing game with elements of a shooter. There is no party in the game: the player only controls Edge on the back of his dragon, who is in fact the playable character in battles. Edge moves around through the game's fully 3D world by riding the dragon. In towns and some dungeons Edge can also move on foot. During battles, the player can either choose to shoot with Edge's gun, or use one of the many special attacks of the dragons.

The battles do not work exactly like in an action game, but occur in real time: the player has to quickly choose an ability to use, and also move around to attack enemies from the sides or from the back, at the same time trying to avoid their attacks. The dragon receives experience points for fighting and also gains levels. The player is able to customize the dragon by assigning to him one of the four available dragon classes, that will determine his attack power, speed, etc.