In an interview with game's design Tetsu Takayashiki, he was asked why the team chose to develop for the Game Boy Color instead of more powerful hardware. He responded: "After Star Ocean and Star Ocean 2nd Story, it was decided that we would make Star Ocean 3 for the PS2. The question then became how to fill in the gap while we waited for that project to begin. From the beginning, our plans were to make a compact game."

In the Gravis Desert is a cracked structure. If the game is being played on a Game Boy Color, there is no way of entering, however, if playing on a non-color Game Boy, there will be an opening. Inside is a room that has a character give the Hero the choice to open one of the two chests in the room, both containing rare power-ups.