The player then assumes the role of young Cal as he is instructed in space ship piloting by the digitized personality of Commonwealth Navy captain Jefferson Clay, a character familiar from the original I-War.

The story then fast-forwards 15 years showing a now-adult Cal Johnston with some of his fellow inmates escaping the prison space station, where the core gameplay begins.

Other groups in Hoffer's Wake begin to notice his work, and as he advances in fame and fortune he learns more about the current situation affecting the Badlands.

They conclude that the most effective action would be to find help outside of the Badlands, so they attack and secure the Santa Romera Jump Accelerator, a highly advanced piece of technology that allows travel over significantly longer distances than even Lagrange points.

Cal arrives in the Fomalhaut system in the Gagarin Cluster to find much the same situation as in the Badlands: oppressive corporate rule, roving Marauders, and a desperate need for assistance.

The story takes a sharp turn when, against Caleb Maas's wishes, corporate scientists activate an alien artifact that Cal himself stole for them, thinking to use it as some sort of weapon.

In free play, Cal can act independently, move throughout the Hoffer's Wake system and eventually the entire Badlands Cluster, and steal cargo.

Edge of Chaos gave a nod to Elite style gameplay by adding free roaming piracy to the Independence War games' universe.