After completing the campaign, I've come up with several questions and speculations---if anyone is interested in discussing them, please see the Spoiler box below:
1) Early on, in the "Warnings" mission, you are following the Truth further into the Betelguese system and 4 Vasudan fighters (Capricorn) and 4 Hercules fighters (called Psi or Phi) warp in. The Vasudan says, what you're doing will lead to the death of us all, and of course they attack you when you won't hand over the containers. This Vasudan guy sounds pretty similar to the Vasudans encountered later, spouting off about the end of the world, etc... so I thought, maybe the Splinter Vasudans went back in time to intercept the Sync drive? But this doesn't seem possible: a Hercules wing would not appear with the Vasudan Capricorn wing if the latter group were Splinter Vasudans.
Now, one might also speculate that Capricorn and Phi just showed up with similar orders to the GTD Carthage... but this doesn't add up either, because later on when the Carthage attempts to arrest everyone, the Carthage itself says, essentially, "you're suspected of illegal activity, what are you doing with the cargo?" etc. So it seems like Capricorn and Phi are not associated with the Splinter Vasudans, nor are they linked with the Carthage. So who the hell are they?
2) At the very end, when leaving the Knossos, what system do you end up in? Back in Terran space obviously, and probably many years after the Second Shivan Incursion, but is it a known system?
3) After everyone skips ahead 3 years the first time, and then when you gradually stumble upon the Vasudan transport and the Faera, neither craft communicate verbally with Alpha wing. So, are they communicating or taking orders from the Persistence? Or are they simply acting on their own? If you assume the Persistence was giving them orders, this leads to a logical flaw: if that were the case, the Faera would not have fled into the final Knossos node. (And the Vasudan transport would never have wandered off on its own earlier in the campaign during the mission where you find the box containing Sync.)
Perhaps Shivans were occupying both of these vessels? The derelict Vasudan transport you find starts itself up mysteriously, and tags along. It then helps tow/repair the Faera, which in turn is critical to finding the Sync box when it's lost in the nebula (detached from the Raikan). And someone in your party even suggests that the Persistence is needed to find Sync since their systems are synchronized in some way. And notice, once you find the box, no orders are given at all to Faera, it simply grabs the box and brings it back with you. So maybe Shivans are controlling or are inside of the Vasudan xport and the Faera after you find them... that would explain why the Faera willfully entered the node at the end. Basically the Persistence was used as a pawn by the Shivans (and ironically, the Persistence itself used Alpha wing and others as its own pawns.)
...sh*t still doesn't add up...
