Taking a much-needed break at home after my semester wrapped up, FSPort, MVPs, FSPort MVPs, and ST:R were all released, AND I had vacation time.
So I've been following this thread, but not replying very much. I do want to say thanks so much for all the praise, and I'm glad most everyone has been enjoying it and its storyline.
Re-read the command briefs for the last mission again. Given what we had to work with, that's the story that brings together all the elements of the original Silent Threat: rogue GTI, the appearance of the Hades, ghost ships, etc. Given what we had to work with, I think it's pretty solid.
Like Goober said, it's not that the GTI was inexplicably anti-Vasudan, it's that the GTA was suddenly pro-Vasudan, after fourteen years of war. You can see a lot of that sentiment in Exodus and Secrets Reborn. Behind the scenes, we're looking at that kind of fracture in Terran politics that contributes to the ultimate dissolution of the GTA. During reconstruction some Terrans want a full alliance, some want segregation, others merely tolerate the Vasudans and some are outright hostile. It took thirty years for a true Terran-Vasudan Alliance to gather enough steam to become the dominant power in the galaxy.
Imagine the politics of unification here on Earth: Apartheid, the Civil Rights movement, the Soviet Union breakup, the European Union creation. It's a complicated issue, and the GTA's post-Great War position probably wasn't a popular one.