Sorry about not posting back there.
Anyway, I've just been brainstorming my Idea for a Pony Mod for FS2 and I finally got it:
It is the year 2403. Equestriankind has moved into space, and is currently engaged in a war with the Canid Race, a war which has raged for 15 years, longer than any war ever seen.
But there is commotion in the home system of Equestria.
The Mare in the Moon--reinstated in 2101--has vanished once again.
And strange, death black ships are attacking Equestrians and Canids, unprovoked, and at random.
They herald the return of a great evil, and if these races want to stop it, they must stop fighting and join forces.
The Shivans are returning.
Nightmare Moon, and Radiant Malevolence, Celestia's Evil Form, have returned.
Locust Plague, Knight Mare, Pestilence, Pitch Black, and Solar Eclipse, five malevolent generals from the War of Discord, fought many years ago, have returned, and they bring with them the six Elements of Discord from that war, as well.
But there are others that have returned, from centuries of cryogenic sleep, many celebronies, some military officials, and several ordinary Ponies.
And among them walk the Mane 6.
And Pinkie Pie.
And these warriors, and more, must battle the Shivans, or witness the fall of two civilizations...
That is the story of My Little Freespace: The Great War.