Not much information is given by Square-Enix about the game's storyline but some hints are given. The main character of the game is Rush Sykes who saw his sister Irina get kidnapped by some mysterious soldiers. Rush then goes out on a quest to save his sister. Also their is another character called The Conqueror who has some connection to Rush and is a person who is trying to collect all the remnants in the world.
Here is the story shown on the Official North American website:
Rush and Irina are the children of scientists researching the esoteric Remnants. One day, Irina is kidnapped right before Rush's eyes. Who are these strange men? Why have they taken Irina? Soon, joined by the marquis of the small city-state of Athlum, Rush chases after the criminals in search of his sister.
Meanwhile the world is being thrust into confusion as ruling powers bicker over dividing the Remnants' power. Out of nowhere, a mysterious man who calls himself the Conqueror appears, escalating tensions over one question: Into whose hands will the power of the Remnants fall? Before he know it, Rush find himself no inly wrapped up in this international intrigue, but somehow connected to the enigmatic Conqueror...
