Many years ago, the Allied Spirit Army fought the malevolent Imperial Wizardry in a prolonged war. Neither side could gain the upper hand until the Imperial Wizardry designed a weapon with too much destructive power. Causing the planet's axis to shift, the deployment of the weapon resulted in the melting of polar ice, which led to a world-wide flood. Four wise men designed a mechanism that allowed the planet's four continents to float above the water. For generations, the secrets of maintaining the mechanism have been passed from the wise men to their descendants. But now, the last of those are gone, and the planet begins to sink into the vast ocean.

Eon is a young man who lives on the continent of Shilf with his foster father. One day, he discovers the powers of a magical orb he found when he was a child. Seeing these powers, Eon's foster father realizes that he might be connected to the wise men of the past. Eon must find the only person who can fix the continent-raising mechanism, and prevent a terrible disaster.

The Granstream Saga is an action game with strong RPG elements, and a spiritual successor to Gaia games. The player controls Eon as he explores overworld and dungeon locations, which are presented in overhead-viewed 3D. Battles are one-on-one; whenever an enemy is encountered, the view is zoomed on the combat participants who must fight each other until one of them emerges victorious. Eon can use swords, daggers, or axes against his enemies. He has a variety of attack moves at his disposal, including combos, shield-breaking abilities, etc.; he can also actively guard and cast magic spells. Leveling up, which increases Eon's attributes, occurs at set intervals throughout the game rather than from accumulating experience points.