The Second Storys gameplay is broadly similar to that of most RPGs. The player goes from town to town and dungeon to dungeon, following the central story and occasionally branching off to perform side quests. Characters gain Experience Points from battle and level up as a result, becoming gradually stronger as time passes and more battles are fought.

However, The Second Story is a member of the Star Ocean franchise, and as such features various deviations from the standard RPG format. Battles are much more action-oriented: they take place in real time, during which the player has manual control over their character, as opposed to choosing options from a menu. Battles take place on a broad battlefield, over which the players character can move without limit, allowing them to trade blows face-to-face with the enemy or circle around for a flanking attack. The other party members (up to 3 others) are controlled by the games AI; the player may change an allys Strategy to one of six different pre-determined options (ranging from Spread out and attack to Save your Magic Points to Stand Still and Dont Do Anything).