The plot of Fate of Io begins in a familiar context, with civilization as we know it reaching its golden age and businesses expanding in technology and wealth. This superficial facade soon falls as the story progresses through its four installments:

Part I
A renegade group made up of environmentalists and political rebels takes on the wealthiest and most innovative corporation in the world. Their plans get them far, only to reveal that the success of their violent insurrection comes at a high price. We are introduced to Syne, Delloran, Enna, Cade, Rheya, Wallace, Benivalle, Dantalian, Hyde, and Kydran.

Part II
The story starts anew in a completely different setting, when the heir of an underground empire is imperiled by an ancient enemy. She finds unlikely friends to help her return home, yet even there she finds that danger is closer than anyone has realized. We are introduced to Ko, Brooke, Rush, Kory, Paerda, and Tyrus.

Part III
The two groups from Part I and II meet amidst confusion and the emergence of a traitor. They must all question their own motives and work together to stop him. We are introduced to Miriel.

Part IV
Everyone enters a much-needed period of recovery, but it is subtly interrupted by a new threat to the very foundation of civilization. Long-forgotten history is uncovered in the race to prevent disaster. We are introduced to Aequus.