Ten years after the events of Crackdown 2, a terrorist attack from an unknown source kills power around the entire world. The Agency is thrust back into action after the attack is traced to the city of New Providence, controlled by the mysterious organization Terra Nova, led by Elizbeth Niemand. The player characters - super-powered Agents - are called into the field by Director Charles Goodwin (Michael McConnohie) and led by Commander Isaiah Jaxon (Terry Crews) as a last resort to dismantle Terra Nova any way they can. As Jaxon briefs the agents of their mission, their drop ship is attacked by Terra Nova, resulting in the deaths of everyone on board.
Echo, a member of the rebel group known as the Militia, recovers the remains of one of the agents and regenerates them. Heavily outnumbered by Terra Nova’s forces, Echo enlists the agents' help in fighting back by dismantling the companies infrastructure.