Story takes place in the year 777 S.D. The Pangalactic Federation continues it's never ending mission of exploration. When a mysterious signal is picked up within the Alpha Equulei System. A crew of Federation explorers go to the signal to discover whatever is making it. However an attack by a mysterious force causes their ship to crash land on a planet named Equuleus, named after the constellation the Alpha Equulei is located in. The survivors of the crash find themselves on an under developed planet full of candy colored sapient ponies. Now this planet and the entire universe are in danger of a new threat.

This story is set in an alternate universe of Star Ocean: Till the End of Time. Which I don't consider actual Star Ocean canon because the whole Eternal Sphere plot device. In fact this story takes place in the Star Ocean: The Last Hope universe. Which isn't set within the Eternal Sphere program.