I hope fdev gives us a rather grounded next step in the story. After Obsidian's remark about goid zombies I thought about Salvation being controlled by them. But that would be cheap writing: "the guy nobody has ever seen turns out to be a traitor... dam dam dam!!" - cheap twist.
Also, "It was the AI all along". It worked for System Shock, but then again: we had no personal, emotional involvement here, so that kind of betrayal won't shock anyone.
Guardian AI by accident and sheer presence of stuff re-initializing and then acting in ways favorable to the goids? Too many coincidences for my taste.
Also wouldn't explain how every Goid structure is now able to convert Guardian relics. "Guardian AI did that" would not satisfy me.
OTOH: Thargoids got their buts kicked multiple times and then started researching Salvation's technology to countermeasures seemsbplausible. They're a highly intelligent species after all.
This would also open up the possibility of Thargoids doing the HIP-thing in other systems with active goid structures quite naturally which in turn would put real pressure on us.