In The Aftermath Reboot, I haven't really elaborated of what the Shivans really are, their true nature, the metaphysical or philosophical aspect of that race as what the other FS2 mods did at a certain degree. The only information I followed regarding the Shivans is the one I found in FS1 and FS2. So, I did not really break the canon. There was not much to go on except that they have five limbs and look like insects. The GTVA did not have any definite clue about them. So I went with that beat and treated the Shivans like any other alien race regardless whether they are organic or not in the AFR storyline. Even in the Ben Aguilar Report, the Shivans being organic is not conclusive. Although, Ben mentioned devices being "surgically" grafted but that is just his words. The AFR GTVA was not concerned about the nature of the Shivans other than they are the enemy. Formidable but just an enemy nonetheless. In other words, every character from the High Council, High Command, down to John Richter are clueless.
Some aspects about the Shivan nature... my opinion
The Shivan juggernauts, the Bhaal command crafts, and the Lucifers are not ships. They are, in fact, beings of the Shivans themselves, their bodies. The Shivan thralls that crewed the Shivan destroyers, corvettes, cruisers, and the fighters are just creations, manufactured and also sentient but controlled. These thralls are a combination of the organic and machinery. The Shivan beings (however and not the thralls) are not of the strictest sense organic but something of an inter-dimensional element. They can be described as energy-based beings but having limited organic components and outer physical exoskeleton shells of strong semi-metallic material. The organic part serves as a nervous system to control the solid physical parts like engines and weapons. They have the ability to manipulate any form of energy and even matter itself as they demonstrated in destroying a star and arming the Shivan Subspace Bombs with an explosive catalyst of something similar to the energy used to trigger a supernova. But the Shivans don't destroy a star to defeat an enemy. They need supernovas to "grow" their technologies, to build their warships and also to feed their 5-limbed thralls. The comprehension and perpective, their concepts, the level of thinking of the Shivans are something an ordinary lesser race (humans included) cannot understand. The Shivans are just different.
A little about the style of story telling...
The entire narrative of AFR and TBG from the techroom database, the Command and Mission Briefings, the in-game dialogues, Debriefings, to Richter's diary, are just the words and point of view of these characters. Example, the corvette Avenger. Description says that it is of Terran construction but in reality, these are Rigelian ships. The GTVA lied and the techroom database is not really reliable. Many of you will say that AFR has no plot because you did not find one in the seemingly incoherent "written" narrative and you won't really find it by just reading them. The real story of AFR is "between the lines," context clues. The real plot of AFR is the in-game experience itself, the missions. This is just my style of story telling... I don't declare, I imply and I don't give everything until the very end of the story where the "bits" converge... but then again, I still don't give all the story.
Now, back to the Shivans... my thoughts.
Aside from the physical descriptions observed by GTVA scientists and certain Shivan technologies they managed to unlock and use, the Terrans and Vasudans had not really scratched the surface of what the Shivans really are. The Shivans are more, much more. The Shivan race goes millions of years back when there were no other sentient race in the galaxy had evolved. And there were two... only two races, the "Ancients," which I call the Dulgari in TBG, and the Shivans. These two races were in harmony and the fact that both use subspace travel is evidence of technological sharing. When Humans and Vasudans came to be, the Ancients and the Shivans visited Earth and Vasuda. They had been observing us for a very very long time, monitoring us in secret. The Shivans, on the other hand, left some relics and artifacts about subspace technology on the Vasudan planet. The Shivans may have interacted with Vasudan primitives. The indications of this is the fanatic HOL who revered the Shivans as gods. It is curious that the Terrans and Vasudans discovered the same subspace technology. The Shivans may had left something for the Terrans as well. However, the Ancients were furious about the Shivans actions in "leaking" the subspace technology. For whatever reasons, we humans cannot comprehend. And so a conflict sparked between the Ancients and Shivans and lasted for thousands of years. The Ancients were defeated but not annihilated for a truce between them was made. The Shivans themselves were almost destroyed in that war. Once again, the Shivans and the Ancients were united but in precarious relationship. These two races became the dominant ones that covered three-fourth of the galaxy and oversaw/protected hundreds of other lesser spacefaring races. They formed the "Grand Galactic Union" (in their language).
The Shivan Planet in AFR, by the way, was not their home planet but just an outpost. The GTVA only assumed that it was. The context clue: an earth-like planet, something is amiss. The GTVA also wrongfully assumed that Grond, the Royal Sathanas, is the leader of the entire Shivan race. Royal Sathanas --- again, the GTVA's way of naming things, another context clue showing the AFR GTVA was screwed up.
Now, fast forward to FS1. The Shivans observed the Vasudans and Terrans in their development while forbidding the other lesser spacefaring races to interfere. The leader of the Ancients, Grimzar, suggested that the Terrans and Vasudans had great potential and planned to let them join the Grand Galactic Union. So they appointed a Shivan supreme controller, Grond, to do a monitoring.
When Grond found that the Vasudans and Terrans discovered the ancient relics of subspace technology and later used it, the very reason that started the great Ancient-Shivan War and almost destroyed his race, Grond decided that these two lesser races were unworthy and took it upon himself to erradicate these barbaric Terrans and Vasudans. His decision was against the consensus of his superiors for he was there only to observe. Nevertheless, Grond gathered his Shivan fleet led by a Lucifer destroyer and wreaked havoc on the Terrans and Vasudans in the first Shivan War. Grond's plans were stopped in its tracks with the Lucifer's destruction but that did not deter him. He amassed an even larger fleet and struck again which led to the events of FS2. But as the war went on, Grond was aware that he will be stopped (or delayed) again. So, seeing that his war with the Terrans and Vasudans, will not progress, he turned his attention to detonate the Capella star to harvest more energy needed to begin building an even larger fleet, literally to "feed themselves." Grond was already contemplating a third and ultimate strike. This led to the events in AFR.
In the meantime, news of Grond's insurrection reached the leadership of the Grand Galactic Union. The Shivan Prime Controller, Draktar (supreme leader in the Shivan language) went to investigate and saw the devastation. But instead of sending a Shivan force to counteract Grond, Draktar used his power of the mind to manupulate a certain wayward mercenary. The mercenary was John Richter. Draktar guided Richter in the Third Shivan War and ulimately destroyed Grond.
Oh, one thing I overlooked. Remember the hundred of Juggernauts in the Capella supernova remnant? These were Grond's fellowmen, his "compadres." He swayed them to his side believing that the GTVA will become a threat sometime in between FS1 and FS2. And indeed, he was right... in a sense. The GTVA had advance to a level that the Shivan Warships, including the Shivan beings, were nothing but tin foil. You can say that it was a growing concern for the Shivan people. Nevertheless, in the end, Grond's forces were decimated and his Shivan supporters or compatriots (the other Juggernauts and Lucifers) were killed. How many Lucifers and Sathanas were destroyed in AFR?
Draktar, the Shivan Prime Controller, he who have lived for millions of years, was hurt in having seen his people, the Juggernauts, Bhaals, and Lucifers, killed in Grond's stupid little war. But Draktar never blamed the GTVA. To his judgement, it was Grond's doing. The Terrans and Vasudans only defended themselves but many of his Shivan citizens were lost.
(Do not confused the Shivan thralls as the Shivan citizens themselves).
Come to think of it... with the GTVA's level of technology, to easily destroy Shivans, will the Terrans and Vasudans become the next dominating species in the Galaxy? Don't forget the Rigelians from the Andromeda Galaxy... another intergalactic war is in the works, Andromeda versus The Milky Way... However, I ended the Aftermath story in TBG.