*spoilers alert*First time I played the game through, I got owned by the black ships as well... and I loved it...
I was like this game rules
I started over from the begining, and I learned more quickly that the green guys and the black guys are fighting over that battle platform, and when the winner is determined that ur-quan will exicute there path of now and forever... for the black guys... that path is to kill every race that isn't ur-quan.... sooo.... black ur-quan = bad
I started sending in other races to attack the black ships... The Thradash, and Utwig and The Suppox will all declare war on the black ships and take some serious loss to their fleets in the process
But their fights will slow that armada from attacking and killing everything.
The game gives you more then enough time to spend a year to collect minerals and get your battle ship to full power, and at that point you want to get indepth with the plot and stop the ur-quan before they kill us all
If you want my tip... one of the first things you should go is get the portal spawner and get get it fixed by the airaluu (excuse my bad spelling) so you can warp over great distances very quickly... this will save your butt big time