Tales of the Abyss takes place on Auldrant, a planet composed of elementary particles called Fonons . For much of Auldrant's history, only six fonons were known to exist, representing the elements of Shadow, Earth, Wind, Water, Fire and Light; but eventually a seventh fonon, controlling Sound, is discovered. Its discovery brings great chaos: using this newest Seventh Fonon allows one to read the future. One such Seventh Fonist, Yulia Jue, puts in place a future for the world for thousands of years to come, with the promise of unlimited prosperity at its end. This prophecy of the future's set path becomes known as the "Score" and is documented on "Fonstones" scattered throughout the world. The nations of Kimlasca-Lanvaldear and Malkuth have fought over the fragments of these tablets for generations, each uncovering them and hoping to discover the future before the other. Meanwhile, a holy order emerges dedicated to the reading of the Score and the keeping of the peace. This "Order of Lorelei" is headed by a Fon Master and maintains both religious/political and military branches. Finally, the Score and its promise of prosperity lead to a dangerous complacency within the general population of Auldrant; the slaughter of an entire people living on the island of Hod and the destruction of that landmass are countenanced because it was predicted in the Score.

As the game commences, Luke fon Fabre, the son of Duke Fabre of the Kimlasca Kingdom, is 17 years old. He is the Light of the Sacred Flame who is destined to bring prosperity to Kimlasca. Since being kidnapped seven years ago by the Malkuth Empire, he has been kept confined to the Fabre family mansion. The shock of the kidnapping has erased all of Luke's memories prior to the event. One fateful day, a mysterious woman breaks into the mansion and sets off a chain of events that drag Luke into the center of a massive conflict between those who would do anything to see the Score carried out, and those who would see it broken forever.