The point of having organisations set up to run things can be more efficient. The problem is, when there's a head organisation, rebellious forces have something to aim an attack towards.
Galactic High Command has run things in the Galaxy for a good number of years, but now they're facing a problem in the shape of an organisation known as 'The Federation'. This band of heavily armed outlaws has spread across the Soa system, consisting of the planets Cleemalt, Lagto and Cleedos, leaving fortresses laden with troops.
You play the part of Xain d'Sleena (which, backwards, says Aneels 'd Niax - interesting, eh?) - a crack stormtrooper, more adept with the use of firearms and the Exo-skeleton armour than any other warrior in his fleet. You must fly out to the invaded planets and destroy the Federation's forces; but on all of the planets you will find a number of pods containing additional weaponry to fit into your Exo-skeleton, which have been left due to a malfunction by the computer at Central Control.
Once all the planets have been cleared, you must return and check them again, just in case an invasion force has managed to reach the planet.