In Galactic Civilizations II you will be able to play as any of the 10 major civilizations. OR you can create your own custom race to play as (pick out your own portrait, etc.). So there will still be the sand box mode that was Galactic Civilizations.
But the sequel will include a campaign and in the campaign you do continue the story of humanity's rise into the galaxy. Where Galactic Civilizations I started in 2178, the sequel begins in 2225. And where Hyperdrive was the center issue of galactic instability, this time around it's the rise of shield technology.
Thanks to the rise of hyperdrive, the Drengin Empire has made great gains throughout the galaxy and the humans must get together allies to help stop them. But the Drengin have a huge head start on military build up. They have massively powerful disruptor based weapons that just rip through the armor of the ships of the other civilizations.
The humans, however, have a new invention: Deflectors. A basic shield technology that counters the disruptors quite well. So while the humans have relatively few ships, they're able to rip through the vast hordes of Drengin fleets as humans also have Phasors in hand for battle.
But it won't be quite enough. There are just too many Drengin ships. The humans will have to put their diplomatic skills to the test as they bring new allies on board through the campaigns to fight the Drengin menace.
What's worse, there are rumors that the Drengin are actually fighting on a second front in a distant part of the galaxy. The Drengin apparently awoken some sleeping evil that is indescribably horrific. Could it be that the evil precursor race of the Dreadlords have returned?
The campaign in Galactic Civilizations II will not require linear play. I.e. you can LOSE a given mission and have the option to continue to an alternative mission. Obviously if you lose enough missions you'll be facing an onslaught against Earth itself.