1: Speaking if universes dying; The tech description for the Vishnan Proximity Gun says that it uses Metastable Vacuum Decay to operate. . . Why Isn't the universe destroyed when I press the fire button?
There are advantages to the perspective the Vishnans have upon universal physics. The proximity gun conjures
higher vacuum states through quantum fluctuation. These states then nucleate and collapse back to our vacuum state. As the energy state inside the bubble rolls back to our vacuum, the contained energy is released, creating violent gravitational waves and a ring of virtual particle creation.
2: Also, there is a 18-year gap between the Capella supernova and Age of Aquarius, and Samuel Bei has severed the GTVA for it least that amount of time if not more, and he is just a lieutenant commander?
Is he just a bad pilot or did something happen, and if so, what?
O-2s (lieutenant JGs) are often 23-25, whereas O-4s (lieutenant commanders) are often in their 30s. Bei isn't too far behind the curve. He's clearly lagging a bit but it's not unbelievable.
From whats been said so far it kinda sounds like a lot of species have since been om nom nommed by the summed psyche thingy. Why is it so critical that more be manufactured? Is there some critical mass that they need to reach for some reason? Alternatively, is absorption into the summed psyche mutually exclusive with being 'worthy interhitors of the brahmans'?
The Great Psyche is in quarantine. If no new species rise up to take on the mantle of the Brahman, to create a new great cosmic order, if in fact the universe falls entirely under Shivan 'gardening' and the Psyche remains eternally aloof and isolated, what future is there for great thought? What high thoughts will ever be thought again? Eventually even the Psyche will run out of possible states. Can you imagine that future for cognition? That dead, sterile end?
It's easy to paint the Vishnans as parasites, manipulators, or creepos. But they are enlightened. They do in truth have access to planes of cosmic knowledge we don't. Trying to grasp their motives is a bit like an ant trying to figure out why a scientist is gene splicing it.
Where are the remnants of other races destroyed by Shivans? I'm talking about their potential noospheric remainder. Through the milions of years they were probably thousands of destroyed races, and some of them were probably Nagari-sensitive like Terrans and Vasudans. If Bosch and his fellows were enough to merge their consciousnesses into entity known as Ken, they were not the first. The Nagari should be quite "populated" with such beings, but it's rather empty. Is this caused by Great Darkness?
That's an awesome question! The Shivans are intrinsically hostile to cognition and would probably degrade such remnants over time, but it'd be cool to see what's out there.
What was UEF's emergency protocol if Shivans return?
Their protocol was to prevent that return. Failing that, fight with very little chance of success, and probably scatter Sanctuary-style. SHAMBHALA's material component was originally thought of as an anti-Shivan countermeasure.
Will we see Orestes and Temeraire again in actual missions?
Yes!
Oh yeah here's one that I need to know because it drove me bloody loopy in real life; who the [BEEP] was 'Truth'?
A disenchanted GTVI officer or affiliate (maybe a contractor or intelligence-adjacent personage). Or so I surmise.
Calculated by what? By the multiverse itself? I'm getting hints that direction re: Rechnender Raum, "Calculating Space." My superficial research into that term isn't bearing a lot of fruit, though, because I'm not sure what you mean to imply by it.
When the Brahman instituted the Terminal Protocol they needed a countermeasure, an immunity, to hold back the Great Darkness. The Shivans satisfy that need.
Is the multiverse being simulated on some other substrate we can't see? Or is the multiverse itself the its own substrate, the calculating space? What is it calculating? Why should it calculate anything at all?
After the Dawn War finished the Brahmans rose up towards enlightenment. In the process they created the panontos, a space built from multiple universes within the multiverse and optimized for thought. At higher levels of understanding it is possible to treat the universe computationally, and to render it more suited for computation. Causality flowed freely between what we would now call universes, and causality itself could be massaged. Subspace is an example of a computational convenience: it is highly energetic and allows information to move faster than it could in the ordinary universe.
Why is the terminal protocol failing? Why is there manifold necrosis evident in the SABADA YEAR data?
This is a good question. One answer is the problem of tolerances. If the Shivans generate too many false positives, they exterminate all incipient life. If they generate too many false negatives, the universe is overrun by defect-strategy hegemons which wipe out diversity and inevitably compromise the interconnectedness of the subspace network (because they use destructive firewall strategies to try to protect their portions of the node network). But worst of all from the Shivan perspective is the
survival of a species which should have joined the Summed Psyche, a 'creator of communities', a befriender of enemies. Because what happens if one of
those takes over a given universe?
It ends up in manifold necrosis. They become vectors. You can see this in Universal Truth 1, where the Shivans and Vishnans argue over the propriety of allowing the humans to survive: the Shivans say they're destroyers, the Vishnans say they're creators, that they have 'potential', that they can equate to the Brahmans of old.
The Vishnans want to give the humans a chance at enlightenment. They want to rebuild what was lost. The Shivans think it's a completely unacceptable risk.
Ok. I got to know. What does the Great Attractor have to do with all of this, or was that just a throw-away line?
It's a big thing out there and someone made it.
Will the elders be allowed to remain free after the surrender of the UEF or are they all heading to Guan-Laramis bay for further study?
MORPHEUS must proceed.
Would the elders sacrifice themselves in order to ensure the success of Shambhala?
Absolutely.
Discounting hostile aliens does the GTVA even have a long term future?
The capture of Sol may relieve some political pressure in the short term but it looks as though massive changes are required to the GTVA command structure. That is before we even get to see whether the promises match the reality regarding the benefits of annexing Sol.
It's possible: I don't think the GTVA as it exists now would be an enduring government, but it's certainly a pragmatic response to a very hostile universe. I would go so far as to say that the GTVA's soft power crisis is one of the greatest reasons the Elders expect SHAMBHALA to succeed.
Some questions about the Shivans:
-How were the Shivans calculated?
They are a characteristic of universes with good immunity.
-The Shivan entity in Universal Truth says the Shivans "slept beneath the waves" before the dawn war. What does this mean?
The Shivans have in a sense always existed: the Brahman 'summoned' or 'computed' them more than 'creating' them. You can discover a new prime number, but you can't say you made it.
-How did the Shivans become involved in the terminal protocol?
The Brahman set them up as gardeners.
-What would happen to the Shivans if the terminal protocol failed?
There would be no more life for them to garden.
-What is the Shivan Alternative to the terminal protocol?
Ah,
now you're asking the big questions. It would, in a sense, be the FreeSpaciest future possible: the Vishnans would have no part and the Shivans would be the absolute arbiter of the right to exist.
Oh benevolent Oracle, share thy wisdom! 
How aware are the elders of the actual, global involvement of the Vishnans and particularly the Shivans?
Highly aware, in the sense that they communicate with the Vishnans.
What exactly is the nature of Earth's non-spaceship defenses? Considering that both orbital- and lunar-defense "bombed"
pretty hard...
I wouldn't want to pin anything down precisely, but presumably there are lots of weapon platforms and missiles. At a point, though, you've got ask what use stationary orbital defenses are in space: it's not like on the ground where a fixed position can carry a lot of extra armor and guns since it doesn't have to move.
Are we going to see the Elder's Guard again, hopefully not doing a knight-in-shining-armor routine?
They're a chivalric order, but you'll see them again. The Elders are very interested in moral ways of conducting violence.
What is the ACTUAL development state of BluePlanet? No finger pointing, just a summary of were things are at.
Some missions and a lot of prototypes for Act 4. A full story outline right through the end (with plenty of wiggle room in case we hit some fun ideas).
To Battuta:
Yes or No can suffice.
1) Is Project Shambhala something that can break through the Vishnan quarantine and compromise their existence, leaving them vulnerable to the Great Darkness?
No.
2) Is The Great Attractor a manifestation of the Great Darkness? Does it exist in parallel universes?
No, and assuming you mean the Attractor, yes, it has a multiversal component.
3) Can The Great Darkness be summarized as a though-consuming cancer?
Yyyyes. It is of thought in the way that cancer is of flesh.
4) Were the Ancient Monologues remnant echoes of the Ancient presence in Nagari, or were they faked by the Vishnans or Shivans?
I'd take them as authentic evidence.
5) Since consciousness is a fatal flaw at higher computational levels, should we interpret the Great Darkness as "less" than we are? Can it be compared to Bacteria (It being alive) or a Virus (No Metabolism, No waste, No stimuli, must assimilate something that is "alive" to replicate)
The Great Darkness is the epitome of consciousness. It is nothing but awareness, awareness of nothing, achievable only by the highest possible orders of thought.
I could only think of one really serious question...
If and when war in heaven and bp3 are finished, what are the chances I will be left without any real closure and forced to rage quit FS?
BP3 had a couple planned endings and at least one of them provided satisfying narrative closure for the great arcs of FreeSpace. Don't expect to Solve Everything Forever: I think it's important that an ending respect the effort the player has put into learning the rules of the universe, not rewrite all those rules.
A question about the Indus.
So, at the end of BP2, the Indus was a broken ship with her future being either scrapped or in a dockyard for a long time. There is, however, a tech room mention of refit Karunas. What's the chance of Captain Sorensen riding in on an Indus MK2?
I think it'd be super dope. The Indus is probably severely ****ed up and maybe a bit radioactive and what better frame for a revenge ship? It'd be like a radioactive death cyborg.
Can you explain a few probably obvious things to someone slow of thought? 
So, the Shivans are are a natural growth, so to speak. They "cultivate" the gardens of individual... universes? They wish to preserve cognitive diversity, right? So they cull groups that get homocidal, like the Ancients and now the Tevs. Is that why they took Bosch and his officers alive? As samples of diversity?
Shivans are per-universe, Vishnans are intra-universe, and to the extent that Shivans talk between universes it's kind of a covert faculty between animae.
Bosch got the Shivans' attention. They consumed him to create a bridge between their 'intelligence' and ours.
Earlier you said that the Vishnans "...are the post-physical intelligences who have passed through the 'filter' of the Terminal Protocol, emerged as cooperators, and been enlightened into the Great Psyche." So the Vishnans aren't so much a species as a collective of reborn "intelligences" from other races that were once Humans, Vasudans, etc. but have now been enlightened? Isn't Bei technically now a Vishnan?
Yes and maybe, wouldn't that be interesting?
And if the Shivans are there to preserve cognitive diversity, why are the Vishnans called "Preservers"? Are they just an anti-Shivan failsafe?
Both sides see each other as the Great Destroyers and themselves as the Great Preservers, and, also, vice versa. To preserve you must destroy, to destroy you must preserve, etc etc.
The FS1 outro makes it clear the Shivans are both: equally, the Vishnans 'preserve' the worthy but also order the cull of the unworthy.