Two years after The Second Story, Leon, Precis, and Rena have moved to Earth - Rena to study medicine, Leon to study Heraldry, and Precis to work on her inventions. Meanwhile, Chisato and Noel have taken up residence on Expel, with Chisato working to establish the media on the planet. Ashton is still wandering Expel looking for a cure to his curse, while Celine is carrying on her affair with Chris, the prince of Cross. Bowman and his wife Nineh now have a child. Most of the characters have new outfits, and Precis now rides a modified Bobot.
Precis takes center stage in the sequel.
The plot begins when she receives an SOS call from Opera and Ernest, who have disappeared while investigating some ruins on an unexplored planet. Precis jets off to the planet, but her spaceship soon falls victim to the same mysterious circumstances and her communication system breaks down. The other nine heroes are called in to rescue the three missing adventurers and discover the cause of the disturbance. Only one monster appears at a time, though monsters now have body parts that can be attacked individually. While the skill system has also been simplified, it's actually more significant to the gameplay.