Here is a question on my mind:
Could the Mycoid spread? EG from ship to ship, Thargoid to Thargoid, Ship to Thargoid etc.
At the moment I am thinking that the whole of the original Elite Thargoid encounters was a single Hive Ship and that is what INRA defeated. However what if the Hive Ship is nowhere near where Jameson's Cobra lays, as it was still able to function for a time and returned to Miacki (assuming Miacki is even a thing in ED and the Thargoids are not now a purely space based migratory species on many HIve Ships). This would mean there will not be a wreck to find near the Cobra.
I have to say though the INRA logs suggest the Mycoid worked both very fast, and very effectivly which would suggest it would cripple such a ship very fast. But we don't know how large a Hive Ship is or how fast Mycoid spreads beyond the contact point.
My last thoughts about about the nature of INRA and AEGIS. I know they are not necessary the same thing or in the same mould, but I am assuming so until proven otherwise. And this creates a dilemma for me. To me, having to use INRA to defeat the Thargoids would be like having to use the 'WW2 German national socialist workers party', well known by another name that we can't type here, to save you from Aliens. You are being attacked by something that aims to wipe you out, but the thing that is defending you is just as bad, only they and not the ones trying to kill you. The leaves a very bad taste in the mouth. Of course I am still half convinced we started the first war anyway.
But FDEV is good with shades of grey. The Thargoids may just be alien, with a very Athropod mind set, only taken to sentience and high levels of intellect. To them wiping out another species might have no morel implications at all, as they may have no concept of morality. To them it may be seem as completely natural resource competition. I doubt the Wasp or Spider feels anything for the fly. In this scenario there is no negotiation or communication. We are food/resources/ a blocker. And so we have a organisation that is so dedicated to their cause (defeating the Thargoids and saving Humanity), that they cannot let things like morals and ethics get in the way. So people were ruined, scapegoated, murdered to get the bigger job done. And it is justified under a cruel version of 'needs of the many'. But I cannot abide by that. So I will not work for AEGIS. And yet, by not working for AEGIS, I could be helping to doom Humanity to defeat by a far worse foe.
And so I hold out of the hope that the Thargoids are not a totally Athropod like species with no morals we would recognise. As ever, we need a whole lot more information, and a whole lot more history to know where to stand.
EDIT: more stream of consciousness...
I would not be surprised if FDEV have thought on all of this and set things up to exploit it and to see how we react, in a big social experiment. INRA are shown to be a very morally bankrupt organisation doing a very good thing. And then we get given AEGIS. But AEGIS is nothing like INRA and really are just what they say they are. Good guys trying to help and with morals and ethics to boot. But people like my won't help them as we just see INRA.
Further more, it the Thrtgoids really are just evil, and not victims themselves, or as I said above have no concept of morality at all and are just behaving like a hive, then it would make the gun totting, right wing, anti-xeno crowd in the right. And people like me a weakness. And that, more than anything else, is a truly terrifying thought!