If there is a Galactic Civilizations III someday, it’s going to have to deal with a lot of issues in its game universe.
If we look at the story of Galactic Civilizations as a 5 chapter (so far) novel you’d have:
Chapter I: Galactic Civilizations: The humans develop Hyperdrive and its technology spread to the other 5 major space-faring civilizations (the Drengin, Arceans, Yor, Altarians, and Torians).
Chapter II: The Altarian Prophecy: Shows us that long ago, there were other races of powerful beings that battled throughout the universe. One of these beings, known as Draginol, used a powerful object known as the Telenanth to create a precursor civilization that came to be known as the Arnor. Draginol and his peers eventually disappeared for reasons we do not yet know leaving the Arnor as the guardians of life. Draginol’s presence, however, for reasons we do not fully understand still, resulted in the Arnor, the Altarians, and humans being visibly similar in appearance.
Chapter III: Dread Lords: This chapter opens up the long-awaited war between the Drengin and their allies (notably the Yor) and the Humans and their allies (notably the Arceans, Torians, and Altarians). The Drengin accidentally free the Dread Lords from a prison located in a pocket universe where the Arnor had put them and they begin to wreak havoc.
As a result, the humans and their allies are forced to deal with the Dread Lords (which they’re successful) only to be beaten down by the Drengin and Yor.
Chapter IV: Dark Avatar: Life is good for the Drengin. Arcea is occupied. Toria is occupied. Altaria has been bombed into submission and only continues to fight on through the Altarian Resistance. The humans, always clever, have managed to keep Earth protected by using an Arnorian shield to produce a forcefield around the planet.
But the Drengin Shock troops, known as the Korath, are insisting on the extermination of the defeated. The Yor support this as well. The Drengin, by contrast, “merely” want to enslave the defeated.
It turns out that the Dread Lords have been pulling the strings of the Korath and the Drengin manage to fight them to a stalemate.
Chapter V: Twilight of the Arnor: The Korath are slowly beating back the Drengin Empire thanks to their relationship with the evil Dread Lords. Luckily, a human expeditionary force has found the last Arnorian who provides aid to defeat the Dread Lords once and for all and ironically saving the vile Drengin from their genocidal brethren.
At the end of Twilight of the Arnor, the evil Drengin reign supreme. The Earth is still protected behind an impenetrable forcefield but is not a strategic factor.
How’s that for a depressing point to leave off?
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So where does Galactic Civilizations go? The story still has 4 more chapters in my mind with the last chapter having many possible endings to it.
One of those endings results in the Yor becoming the dominant force in all the universe (not just the galaxy). As someone who has a healthy interest in astronomy, the sheer scale of the galaxy, let alone the universe is something I take very seriously.
In the dark future where the Yor take over, there are no living creatures anywhere. The universe itself becomes sentient via a Yor-invented material known as “the substrate”. Essentially it is material that spreads across the universe converting all matter into this material in which the Yor come to exist within.
The best (and still poor) analogy would be that this material is used to turn all matter into a single massive computer and all consciousness exists within this “Matrix-like” existence --- except there is no biological life. No one is connected to VR but rather all conscious reality exists within it with the collective intelligent of the the Yor being able to spread the substrate to all places at once through the folding of space.
Nothing in this scenario would even exist in the physical, material world anymore. All life would exist in the virtual sense within the Substrate. THAT is the goal of the Yor.
The Yor, of course, are right now merely synthetic organisms that exist still as individual physical entities in the material universe. They do not yet have the means (technological or otherwise) to realize their dream but that is their goal.
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Of course since we’re humans, the fate of humanity in the form of the Terran Alliance (those darn earthlings) will be the center point of the concluding chapters. But they are an even greater threat than the Yor (and if we get to make GalCiv III you’ll see that). The Thalan, in fact, are actually a race of beings from a parallel universe who have figured out the means to travel to other universes and managed to enter our universe at a point before the humans destroyed the universe (though, “destroy” obviously will have to be explained since one man’s “destroy” is another man’s “transform”.). The universe, being over 13 billion years old and unimaginably large can’t be “destroyed” in the conventional sense.
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From a GAME point of view, however, what makes me exited for a future Galactic Civilizations game are the artifacts which will allow players to do a lot of crazy things in game that are fun and interesting. But that’s for another discussion. 
Piece of Trivia:
The aliens in Galactic Civilizations II were designed and modeled by Paul Warzecha. Today, he is the lead character modeler on Diablo 3.
