Twenty years after the events of the Star Ocean video game, Ronixis J. Kenni and his son, Claude C. Kenni are on a mission to investigate a newly discovered planet. While investigating a strange machine with a mysterious energy field, Claude finds himself transported to the planet of Expel. He wakes up in a forest, where he meets Rena Lanford, a young girl being attacked by a monster. After defeating the monster with his phase gun, Rena takes him back to her village of Arlia where he is declared to be the legendary "Warrior of Light" who will save Expel. The planet is in peril since the landing of a large meteorite, the Sorcery Globe, which has caused monsters to spawn around the planet, as well as numerous natural disasters such as earthquakes and tsunami.

Claude refuses to accept he is this warrior, and leaves to try to find someone who can help him go home. In the next town, he learns Rena is in danger from her childhood friend Allen. He rushes to rescue her and finds Allen under the control of a magic crystal. With the crystal destroyed, Allen returns to normal. Realizing the crystal is tied to the Sorcery Globe, and wondering if it can help him get home, Claude decides to travel to El Continent to investigate it and Rena goes with him. Along the way, the meet Celine Junes, a Heraldic Magic user and treasure hunter who tricks the pair into helping her steal the treasure from a cave. The treasure turns out to be a book written in a language none of them knows, so Celine decides to stay with the pair to try to find out more about the book. They group is later joined by Ashton Anchors, another swordsman whom they first encounter in a cave trying to defeat a monster terrorizing a nearby village. Ashton attacks a two-headed dragon, thinking it is the monster, and after he trips the dragon fuses itself to his body, leaving him with the two dragon heads coming out of his back. Ashton makes the group go with him to find the King's Teardrop, blaming them for "distracting him" during his fight and causing everything. After they get there he learns that using the magic power would kill the dragon, so he refuses to do it and joins the group until they can find a way to remove the dragon without causing it any harm.

In the town of Linga, they meet Precis, a young girl inventor who develops a crush on Claude and is oblivious to Ashton being in love with her. They help her cure her friend from a dying illness, and afterward Precis decides to go with them to Lacour where they hope the famous Dr. Leon can answer their questions about the Sorcery Globe and Celine's book.