Claude Kenni is a young man who recently joined the Earth Federation, following the steps of his father. A strange energy has been spotted somewhere on a distant planet, and Claude and his father go there to investigate the matter. However, Claude gets sucked into a portal and ends up on a mysterious planet, in the middle of jungle. There, he sees a young girl threatened by a ferocious beast. That young girl is Rena Lanford, an inhabitant of the planet and the second protagonist of the game. The dangerous encounter makes the paths of the two heroes cross, and they continue their journey together.

Like its predecessor, Star Ocean: The Second Story is a Japanese-style role-playing game with action-based battles. Combat takes place in an arena that allows player-controlled characters to chase down or run away from enemies, as well as unleash special moves that damage any enemies in a large area of effect. Characters can learn various skills during the game, and become an expert alchemist, blacksmith, scientist, etc. They can also produce their own items (like for example making armor from iron ore if the character has the appropriate skill).

Another stand-out feature of the game, carried over from the previous installment, are the so-called "Private Actions". The protagonist can talk to other party members and raise or lower their sympathies, influencing their performance in battle and ultimately branching the plot and affecting the ending. The games has eighty slightly different endings that depend on the player's choices during character conversations throughout the game.