The game takes place in the distant future. The player takes the role of a survivor of a faction of humans known as the Tograns, whose society was decimated after their homeworld became engulfed in the civil war between the Freedom Guard and the Imperium (who were once both the Sprawlers and the Jovian Detention Authority (JDA) from Dark Reign 2 respectively). As one of the last remaining Tograns that set off in hopes they might find a new refuge to rebuild and carry on the words of Alpheus Togra (a famous research scientist and philosopher), the player is presented with an opportunity to go back through time and prevent the death of the founder, Togra, using an advanced probe launched by him just prior to the destruction of the planet Strata-7. To use the device, the player must first demonstrate their worth by achieving victory in simulations of famous battles between the Imperium and the Freedom Guard.

The thirteen missions play out the events from the first skirmish between the Imperium and Freedom Guard up to the battle for and destruction of Strata-7. The missions may freely be played from the perspective of the Imperium or the Freedom Guard. In the thirteenth and final mission, the last Togran, the player, is sent back in time using the Chronomachine to Strata-7, and must use the weapons and technology of both the Imperium and the Freedom Guard to combine a force that will defeat both sides and prevent the complete destruction of Strata-7 and the death of Togra.

In the expansion, Rise of the Shadowhand, the story depicts the increasing desperation and despotism of the Imperium after the emergence of the Tograns as a third credible faction. After a massive Imperium assault on Freedom Guard space, a fleeing transport stumbles upon a planet, at the other side of the galaxy, where the Imperium secret police, the Shadowhand, have conducted major research. By coincidence, the Shadowhand simultaneously is faced with losing control of its advanced units due to the malfunction of their guiding AI, Osiris.