Like most of us, when I did the ancient ruins mission I stopped reading after the 3rd planet because my head just felt numb. However with the Thargoid war I went back and looked for info about the Guardians sites and weapons. So one thing led me to the next and I stumbled upon a video with all the decoded logs and from what I gathered.
The Guardians developed genetic tech that allowed them to create these “animals" that first were used as basically heavy machinery, then they went micro and built organisms that boosted the Guardians immune systems and helped them fight things like cancer and all was good.
Then some scientists started to realize that their society was advancing towards a more sedentary society with them being historically nomadic or semi nomadic. A subset of the society decided to go back to their natural roots creating a new naturalistic religion based on their technological skills with genetic manipulation. And then a schism of sorts occured where a subset of the Guardian society decided to stay in their stone cities, what we now know as ancient ruins; while the other more naturalistic subset went on to create or rather grow biological based cities, which to me sound a lot like those creepy Thargoid "dead husk" cities.
So would it be too crazy to assume that the Guardian civil war was fought by "Stone" Guardians, who we now know as well, Guardians using steal ships. And "Naturalist" Guardians using living ships which we now know as Thargoids?
With this in mind I could see 3 different scenarios.
1. The Thargoids defeated the Guardians in their civil war and they being nomads didn't occupy the devastated Guardians planets but evolved into traveling inside huge generational living ships moving away, from the bubble, give it a couple million years and their genetic experiments moved them into changing their bodies to survive the hell of outer space pushing them into fusing with their ships which is why we don't really see "Thargoid foot soldiers'' because there is not such a thing and in turn this change also made them dependant on caustic environments. Then they notice that a squirrel based species is starting to poke around their defeated forefathers tech and they go "Know what, we don't want another war" So they don't outright attack humanity but strife to keep us away from guardian tech meaning they target and attack commanders carrying relics. And then a bunch of sea squirrels decide to settle in their very well crafted caustic planets and they go "Well this just won't do" and attack humans beginning the Thargoid war 1.
2. The Targoids were originally designed as living weapon to fight in the Guardian civil war, however as it happens often, the A.I piloting these weapons understood the prime directive as victory at all costs meaning they just stopped focusing in the costly and hard to defeat other Thargoid weapons and just focused in the squishy Guardian bodies leaving the Thargoids as "Space Guardian cleansing roombas", which in turn meant that when the sea squirrels started to poke a round the Guardian sites, the Thargoids reactivated and well the whole Thargoid War 1 and 2 caustic boogaloo happened.
3. The genetic experiments from the guardians had a bit of a glitch that forced them to evolve into Thargoids who need caustic environments to survive. So what we know as Thargoids are actually super mutated Guardians and whatever Salvation did, called on the more violent Thargoid faction. which looking at their story were probably the "naturalist" Thargoids who were away being nomads, until the wave called upon them as a beacon and now they are back to wipe those really annoying sea squirrels. Which would also explain why they look a bit different to the old Thargoids, and why the old Thargoids didn't really attack humanity but just kinda pushed us away from Guardian tech, maybe to stop us from becoming Chipmunkgoids ourselves or to stop us from calling on the nomad Thargoids.
It could also explain why the Thargoid kidnapped sea squirrels. After all it’s been ages since they had squirrel sized bodies and they thought “hey, maybe these filthy suicidal squirrels hold the key to put our consciences back into practical pocket sized bodies.
And that could also explain why in our very rudimentary translation of very incomplete and probably corrupted, manufactured or falsified Guardian historical records, we can see that the Thargoids claimed to be an older race than the Guardians, with claims in the Guardian territory. Maybe what they meant was that the Thargoids were a splinter civilization claiming to be the original Guardian civilization living by the old ancient ways of being nomads. And their claims on the Guardian territory is more akin to what Jerusalem is to all the Abrahamic religions on earth, basically Guardians and Thargoid fighting over who was more chosen and whose way of life was more right.
