Thankfully they are the good guys. I had a problem with the dark conspiracy angle in 1e. It was fun and made for some good story ideas but way to many novas running around with enhanced senses, telepathy, bio manipulation, mega-int and much more to ever allow a conspiracy like that to stay hidden.
I know a lot would be over looked as people just don’t want to believe their saviors are the bad guys. However that would only go so far.