Resonance of Fate takes place on Earth in the distant future. When atmospheric pollution nearly annihilates life on Earth, the remnants of humanity construct a purification system called Basel. In time, the surviving human population create a civilization around Basel's central tower, watched over by its mechanical core Zenith. Zenith ties human lives to quartz stones, making them immune to the pollution while giving them predetermined social status and lifespans. The three protagonists—Zephyr, Leanne, and Vashyron—form a mercenary group that take odd jobs for the populace of Basel. During their missions, they discover a plan by the city's ruling Cardinals to subvert Zenith's rule, and discover their own connections to the Cardinals' plans.