So there needs to be a story, and since I'm no good at programming and focus on military/business endeavors, I would like to offer a few ideas:
At the end of the game, there were reports of blue machines self-destructing all over their empire. What if there was a pod that had damage to it due to a more inhospitable area and therefore did not receive/follow out the instructions and continued operations?
What if the original red machines de-armed themselves in order to repurpose resources and technology to further colonize the galaxy, and ran into the area that the corrupt colony was established? Nukes would be used to quickly clear dangerous asteroids, plasma used to cut through metals more effectively, explosive material used to blast away rock to access resources... etc.
The original controller purged memory of all military tactics and technology (and its application), as well as got rid of the experimental AI that was used to win the original campaign.
What if the corrupt colony developed shielding technology that allowed it to operate in the hostile environment?
There could also be twists such as humans arriving, or finding life on some of the other planets. Maybe even re-visiting battlefields to salvage research, for example, having and entire battle over which race can salvage APC technology from the crashed APC from the mission "Behind Enemy Lines" so that the races could be more mobile.
Make the machines upgradable; i.e. giving civilian machines rudimentary means of defending themselves. Or being able to shunt power to their motors in order to escape quicker, at the expense of their shields/armor.
