Ys I・II: Eternal Story is an updated version of Ys I II Complete. It introduces an additional mode that re-balances the leveling system for a smoother transition between the two games. It also contains a bonus "Magic World", which contains new characters, a few sub-quests, as well as access to artwork gallery and sound test. Voice acting has been added as well.

This version also introduces changes to the weapon system. In all previous releases of the games a more powerful sword rendered weaker ones useless. In this version, each sword has additional properties: for example, the initial Short Sword can now stun enemies.