For argument's sake, whether or not it actually happens whenever, let's assume the worst case scenario is true. Let's assume it will be proven that certain people at the top of the US government were primarily (if not solely), or at least significantly enough, responsible for 9/11. Assume the government will also be proven responsible for the cover-ups and denials of everything UFO, close encounters, and whatever else (intelligently) nonhuman-related that's been kept from the public. And we can easily assume, for example, that the "magic bullet" theory (authored by Arlen Specter) and the Oswald (as the lone gunman) claim don't apply in the JFK assassination.
Be prepared for even worse and much, much more, if applicable. Assume there is a plethora of horrifying or otherwise extremely shocking information, much or most of which has never been mentioned even once on the most "alternative" web discussion (conspiracy-related) sites, that will be revealed. The obvious question then becomes: What is the most intelligent and civilzed thing we can, or will, do about the gargantuan mess?
In short, don't do what they, the government (as we know it) types and their seemingly endless throngs of supporters, would do. Seek no punishments or vengeance. Don't become them. Let them merge with us, as often as possible, or at least give them a plenty good enough chance to do so. Avoid being ruled by pathology/pathocracy as they (at least now) are. Let truth be its own justice.
The obvious solution is to create a truly new societal-governmental system - one with plenty of and truly effective checks and balances. We only need to ensure, to the best of our ability, that certain despicable activity never happens again. (Essentially that involves real and impeccably verifiable transparency, not rule by secrecy). The horribly primitive "eye for an eye" mentality simply isn't necessary. Whether or not we will be able to implement nonhuman knowledge and methods in keeping psychopaths and sociopaths (if there's really any difference between the 2) out of positions of power is, of course, uncertain at this point. However it happens, when there is strong enough will, there is a way.
What humanity needs most is a new spiritual direction, which includes forgiveness and love. We need enough people with enough humility and honesty to admit that too much of what we've been taught and think we know is wrong, or inadequate, therefore everyone needs and deserves a clean slate, new education... Good Christ I'm tired of restating the same old stuff in slightly different ways.