While flying a space shuttle, Hugh's ship gets seriously damaged after a run in with a crystal dragon. Afterwards Hugh wakes up in a daze inside another spaceship. He is greeted by a mysterious female named Jean. Hugh is soon dropped off alone at a spaceport. Now the player (controlling Hugh) has to locate his two missing shipmates, Cynthia and Nial, and also uncover the mystery behind the enigmatic crystal dragon.

While playing the game, a picture is displayed of the player's current location with the available actions being presented above. Actions include move, examine, take, talk, use item, open door, operate, and place. There is also an option to save a game that is in progress. Players have to explore several areas looking for items, so they can later be used to solve various puzzles. Successfully solving puzzles opens up more locations to be explored and progresses the storyline further.

The various characters were designed by an animation studio, Nippon Sunrise, which Square contracted to do graphical work with the game. At various points in the game the player can talk or listen to these characters, most of which animate as they speak.