I'd like to share few thoughts too...
First, does anyone have any idea, what is behind the third knossos portal, and what was the system in the "DIVE, DIVE, DIVE" mission ?
It could be reasonable to assume, that like the first portal, the second and third were also contructed by the ancients, but for what purpose ?
How many of those devices exists in total ?
Some thoughts about the Shivan fighters, are they actually piloted by the shivans or are they merely "extensions" or drones...
Their fighters look very crampy from the outside, frankly I don't get how the shivans can fit in there..
Why did the first portal led to the nebula ? I could be mistaken here, but didn't it lead to the place where the ancients first encountered with the shivans. So, why is there nebula now ? Nebula, that is remant of the supernova....Was that Nova caused by the shivans too, who knows ?
If that is correct, why the Shivans are intentionally creating supernovas, you have seen the Sathanas do their true job. Command speculated that the Shivans were powering up a new kind of weapon, if so, was the system beyond the first portal another example of Shivan handiwork.
Then at the end of FS2, it was said that the destruction of the star could be the bridge between our universe and theirs. If they are originating from other universe, they must have fleet and power beyond description...